Starting phenix.real_space_refine on Tue Jun 10 12:23:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wc0_8794/06_2025/5wc0_8794.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wc0_8794/06_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_8794/06_2025/5wc0_8794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wc0_8794/06_2025/5wc0_8794.map" model { file = "/net/cci-nas-00/data/ceres_data/5wc0_8794/06_2025/5wc0_8794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wc0_8794/06_2025/5wc0_8794.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} 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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 9} 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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} 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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} 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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} 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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} 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: 7.20, per 1000 atoms: 0.63 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: 2.73 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.19 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: 2.98 Time building geometry restraints manager: 3.23 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: 2.250 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.760 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- 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 : 5.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP A 465 HIS 0.004 0.001 HIS A 206 PHE 0.016 0.002 PHE F 334 TYR 0.012 0.002 TYR E 284 ARG 0.016 0.001 ARG D 351 Details of bonding type rmsd hydrogen bonds : bond 0.17515 ( 484) hydrogen bonds : angle 9.70112 ( 1398) covalent geometry : bond 0.00566 (11633) covalent geometry : angle 1.06244 (15945) 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 : 1.200 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 203 GLN cc_start: 0.8669 (tt0) cc_final: 0.8403 (tm-30) REVERT: A 372 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8836 (mm-30) REVERT: B 239 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8413 (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: 0.7222 (mt-10) REVERT: C 229 MET cc_start: 0.8892 (ptp) cc_final: 0.8595 (ptp) REVERT: C 239 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8263 (mtmt) REVERT: C 249 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8587 (tm-30) REVERT: C 336 LEU cc_start: 0.9202 (tp) cc_final: 0.8795 (tt) REVERT: C 371 ILE cc_start: 0.9376 (mt) cc_final: 0.8939 (mt) REVERT: C 448 GLN cc_start: 0.9400 (pt0) cc_final: 0.8860 (pt0) REVERT: D 293 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7178 (mm110) REVERT: D 372 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8059 (mt-10) REVERT: E 203 GLN cc_start: 0.8856 (tt0) cc_final: 0.8421 (tp40) REVERT: E 219 PHE cc_start: 0.9038 (m-80) cc_final: 0.8806 (m-80) REVERT: E 229 MET cc_start: 0.8308 (ptp) cc_final: 0.8103 (ptt) REVERT: E 411 ASN cc_start: 0.9120 (t0) cc_final: 0.8711 (t0) REVERT: F 206 HIS cc_start: 0.8315 (t-90) cc_final: 0.8097 (t-170) REVERT: F 385 ASN cc_start: 0.9180 (t0) cc_final: 0.8964 (t0) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.2511 time to fit residues: 81.8512 Evaluate side-chains 138 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.061881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.049759 restraints weight = 87132.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.050868 restraints weight = 60251.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.051609 restraints weight = 45190.255| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11634 Z= 0.130 Angle : 0.592 6.609 15945 Z= 0.323 Chirality : 0.043 0.177 1966 Planarity : 0.005 0.051 2061 Dihedral : 12.789 89.380 1928 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.11 % Allowed : 1.28 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.19), residues: 1612 helix: -1.80 (0.15), residues: 819 sheet: -2.15 (0.33), residues: 185 loop : -1.64 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 465 HIS 0.004 0.001 HIS B 206 PHE 0.018 0.001 PHE F 317 TYR 0.016 0.001 TYR E 386 ARG 0.013 0.001 ARG E 392 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 484) hydrogen bonds : angle 5.20681 ( 1398) covalent geometry : bond 0.00267 (11633) covalent geometry : angle 0.59208 (15945) Misc. bond : bond 0.00194 ( 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 192 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 1.377 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: 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: 0.8880 (tt0) cc_final: 0.8643 (mt0) REVERT: A 372 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8883 (mm-30) REVERT: A 410 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9088 (mp) REVERT: B 198 MET cc_start: 0.8990 (mpp) cc_final: 0.8787 (mpp) REVERT: B 385 ASN cc_start: 0.7709 (t0) cc_final: 0.7299 (t0) REVERT: C 239 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8393 (mtmt) REVERT: C 371 ILE cc_start: 0.9377 (mt) cc_final: 0.8642 (tt) REVERT: D 372 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7987 (mt-10) REVERT: D 375 MET cc_start: 0.8677 (mmm) cc_final: 0.8042 (tpt) REVERT: E 219 PHE cc_start: 0.9106 (m-80) cc_final: 0.8867 (m-80) REVERT: E 336 LEU cc_start: 0.9471 (tp) cc_final: 0.9204 (tt) REVERT: F 206 HIS cc_start: 0.8831 (t-90) cc_final: 0.8532 (t-170) REVERT: F 207 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8158 (mt-10) REVERT: F 229 MET cc_start: 0.8444 (pmm) cc_final: 0.8207 (pmm) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.2368 time to fit residues: 64.3676 Evaluate side-chains 136 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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** E 206 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.059320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.047727 restraints weight = 91139.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048734 restraints weight = 63158.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049488 restraints weight = 47609.744| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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= 0.169 Angle : 0.586 7.144 15945 Z= 0.316 Chirality : 0.041 0.132 1966 Planarity : 0.005 0.050 2061 Dihedral : 11.854 89.979 1928 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.32 % Allowed : 2.13 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.20), residues: 1612 helix: -1.13 (0.17), residues: 847 sheet: -1.73 (0.34), residues: 185 loop : -1.39 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 465 HIS 0.004 0.002 HIS C 206 PHE 0.015 0.002 PHE D 278 TYR 0.022 0.001 TYR F 386 ARG 0.006 0.001 ARG E 392 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 484) hydrogen bonds : angle 5.02130 ( 1398) covalent geometry : bond 0.00350 (11633) covalent geometry : angle 0.58580 (15945) Misc. bond : bond 0.00018 ( 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 174 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 1.361 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: symmetry clash REVERT: A 372 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8871 (mm-30) REVERT: A 375 MET cc_start: 0.8568 (tpt) cc_final: 0.7953 (tpp) REVERT: B 198 MET cc_start: 0.9045 (mpp) cc_final: 0.8718 (mpp) REVERT: B 380 LYS cc_start: 0.8277 (ptmt) cc_final: 0.7892 (ptmt) REVERT: C 207 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6984 (mt-10) REVERT: C 371 ILE cc_start: 0.9344 (mt) cc_final: 0.8954 (mm) REVERT: D 372 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8084 (mt-10) REVERT: D 375 MET cc_start: 0.8865 (mmm) cc_final: 0.8190 (tpt) REVERT: E 193 ASP cc_start: 0.8965 (m-30) cc_final: 0.8736 (t0) REVERT: E 219 PHE cc_start: 0.9122 (m-80) cc_final: 0.8771 (m-80) REVERT: E 336 LEU cc_start: 0.9394 (tp) cc_final: 0.8986 (tt) REVERT: E 375 MET cc_start: 0.9079 (tpp) cc_final: 0.8793 (tpp) REVERT: F 206 HIS cc_start: 0.8970 (t-90) cc_final: 0.8683 (t-170) REVERT: F 229 MET cc_start: 0.8593 (pmm) cc_final: 0.8309 (pmm) REVERT: F 416 TYR cc_start: 0.7097 (m-80) cc_final: 0.6871 (m-10) outliers start: 3 outliers final: 1 residues processed: 173 average time/residue: 0.2207 time to fit residues: 56.0102 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 : 1.219 ------------------------------------------------------------------------------- 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: 1.9990 chunk 113 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN F 448 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046986 restraints weight = 94166.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048029 restraints weight = 63922.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048657 restraints weight = 47470.244| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11634 Z= 0.218 Angle : 0.620 9.945 15945 Z= 0.333 Chirality : 0.042 0.136 1966 Planarity : 0.005 0.050 2061 Dihedral : 11.878 88.504 1928 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.21), residues: 1612 helix: -0.67 (0.17), residues: 823 sheet: -1.40 (0.36), residues: 185 loop : -0.89 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 226 HIS 0.006 0.003 HIS E 206 PHE 0.018 0.002 PHE D 278 TYR 0.028 0.002 TYR F 284 ARG 0.004 0.001 ARG E 392 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 484) hydrogen bonds : angle 4.99281 ( 1398) covalent geometry : bond 0.00446 (11633) covalent geometry : angle 0.62048 (15945) Misc. bond : bond 0.00025 ( 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 159 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 1.316 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 207 GLU cc_start: 0.8644 (mp0) cc_final: 0.8384 (pp20) REVERT: A 372 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8905 (mm-30) REVERT: B 198 MET cc_start: 0.8976 (mpp) cc_final: 0.8715 (mpp) REVERT: B 239 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8902 (mttp) REVERT: B 375 MET cc_start: 0.8854 (tpt) cc_final: 0.7919 (tpt) REVERT: B 385 ASN cc_start: 0.7642 (t0) cc_final: 0.7389 (t0) REVERT: C 198 MET cc_start: 0.9170 (mtm) cc_final: 0.8801 (mtm) REVERT: C 207 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6942 (mt-10) REVERT: C 239 LYS cc_start: 0.8646 (pttm) cc_final: 0.8274 (pttm) REVERT: C 371 ILE cc_start: 0.9382 (mt) cc_final: 0.9003 (mm) REVERT: C 400 ASP cc_start: 0.8813 (m-30) cc_final: 0.8606 (t70) REVERT: D 203 GLN cc_start: 0.9350 (tt0) cc_final: 0.8375 (tm-30) REVERT: D 207 GLU cc_start: 0.8214 (pt0) cc_final: 0.6741 (pt0) REVERT: D 293 GLN cc_start: 0.7543 (mm110) cc_final: 0.7242 (mm110) REVERT: D 372 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8043 (mt-10) REVERT: D 375 MET cc_start: 0.8886 (mmm) cc_final: 0.8015 (tpt) REVERT: E 203 GLN cc_start: 0.8913 (tt0) cc_final: 0.8666 (tp-100) REVERT: E 336 LEU cc_start: 0.9460 (tp) cc_final: 0.9167 (tp) REVERT: F 206 HIS cc_start: 0.8915 (t-90) cc_final: 0.8667 (t-90) REVERT: F 207 GLU cc_start: 0.8922 (pt0) cc_final: 0.8713 (pp20) REVERT: F 229 MET cc_start: 0.8611 (pmm) cc_final: 0.8278 (pmm) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.2140 time to fit residues: 50.6572 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 : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 125 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN E 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.058300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046476 restraints weight = 84568.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047543 restraints weight = 57252.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.048349 restraints weight = 42441.566| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4396 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= 0.103 Angle : 0.509 8.968 15945 Z= 0.272 Chirality : 0.040 0.137 1966 Planarity : 0.004 0.045 2061 Dihedral : 11.378 88.884 1928 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1612 helix: -0.12 (0.18), residues: 825 sheet: -0.96 (0.37), residues: 189 loop : -0.55 (0.29), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 465 HIS 0.005 0.001 HIS E 206 PHE 0.021 0.001 PHE F 317 TYR 0.008 0.001 TYR F 416 ARG 0.004 0.000 ARG F 223 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 484) hydrogen bonds : angle 4.31414 ( 1398) covalent geometry : bond 0.00226 (11633) covalent geometry : angle 0.50942 (15945) Misc. bond : bond 0.00007 ( 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 176 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.244 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: 0.6482 (pmm) cc_final: 0.5988 (ppp) REVERT: A 372 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8838 (mm-30) REVERT: A 394 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7362 (mm-30) REVERT: B 198 MET cc_start: 0.8980 (mpp) cc_final: 0.8691 (mpp) REVERT: B 229 MET cc_start: 0.9324 (ppp) cc_final: 0.9072 (ppp) REVERT: B 380 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8946 (tttm) REVERT: B 385 ASN cc_start: 0.8151 (t0) cc_final: 0.7863 (t0) REVERT: C 198 MET cc_start: 0.9041 (mtm) cc_final: 0.8812 (mtm) REVERT: C 254 PHE cc_start: 0.8356 (t80) cc_final: 0.7911 (t80) REVERT: C 371 ILE cc_start: 0.9375 (mt) cc_final: 0.9101 (mm) REVERT: C 376 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8597 (mm-30) REVERT: D 203 GLN cc_start: 0.9458 (tt0) cc_final: 0.8346 (tm-30) REVERT: D 207 GLU cc_start: 0.7967 (pt0) cc_final: 0.6404 (pt0) REVERT: D 293 GLN cc_start: 0.7610 (mm110) cc_final: 0.7343 (mm110) REVERT: D 372 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7500 (mp0) REVERT: D 375 MET cc_start: 0.9035 (mmm) cc_final: 0.7989 (tpt) REVERT: E 203 GLN cc_start: 0.8847 (tt0) cc_final: 0.8519 (tp-100) REVERT: E 207 GLU cc_start: 0.7800 (mt-10) cc_final: 0.6692 (pt0) REVERT: E 219 PHE cc_start: 0.9068 (m-80) cc_final: 0.8655 (m-80) REVERT: E 336 LEU cc_start: 0.9437 (tp) cc_final: 0.9084 (tt) REVERT: F 206 HIS cc_start: 0.8942 (t-90) cc_final: 0.8593 (t-90) REVERT: F 207 GLU cc_start: 0.9169 (pt0) cc_final: 0.8448 (pp20) REVERT: F 229 MET cc_start: 0.8576 (pmm) cc_final: 0.8162 (pmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2181 time to fit residues: 56.1425 Evaluate side-chains 125 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.0020 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.4792 ------------------------------------------------------------------------------- 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** E 411 ASN F 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.044664 restraints weight = 92384.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045715 restraints weight = 61442.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046460 restraints weight = 44968.709| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11634 Z= 0.170 Angle : 0.566 10.215 15945 Z= 0.301 Chirality : 0.040 0.128 1966 Planarity : 0.005 0.048 2061 Dihedral : 11.328 89.723 1928 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1612 helix: -0.26 (0.18), residues: 851 sheet: -0.74 (0.37), residues: 192 loop : -0.67 (0.29), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 465 HIS 0.006 0.002 HIS E 206 PHE 0.015 0.002 PHE F 317 TYR 0.013 0.002 TYR C 386 ARG 0.004 0.001 ARG E 352 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 484) hydrogen bonds : angle 4.57472 ( 1398) covalent geometry : bond 0.00363 (11633) covalent geometry : angle 0.56635 (15945) Misc. bond : bond 0.00020 ( 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 153 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.379 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: 0.6453 (pmm) cc_final: 0.6035 (ppp) REVERT: A 372 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8867 (mm-30) REVERT: B 198 MET cc_start: 0.9006 (mpp) cc_final: 0.8693 (mpp) REVERT: B 229 MET cc_start: 0.9275 (ppp) cc_final: 0.9072 (ppp) REVERT: C 198 MET cc_start: 0.9116 (mtm) cc_final: 0.8727 (mtm) REVERT: C 254 PHE cc_start: 0.8525 (t80) cc_final: 0.8054 (t80) REVERT: C 371 ILE cc_start: 0.9454 (mt) cc_final: 0.9128 (mm) REVERT: C 376 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8693 (mm-30) REVERT: D 203 GLN cc_start: 0.9476 (tt0) cc_final: 0.8760 (tm-30) REVERT: D 293 GLN cc_start: 0.7885 (mm110) cc_final: 0.7592 (mm110) REVERT: D 372 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7552 (mp0) REVERT: D 375 MET cc_start: 0.9096 (mmm) cc_final: 0.8214 (tpt) REVERT: E 203 GLN cc_start: 0.8897 (tt0) cc_final: 0.8455 (tp-100) REVERT: E 207 GLU cc_start: 0.7898 (mt-10) cc_final: 0.6716 (pt0) REVERT: E 336 LEU cc_start: 0.9388 (tp) cc_final: 0.9137 (tt) REVERT: F 207 GLU cc_start: 0.9151 (pt0) cc_final: 0.8716 (pp20) REVERT: F 229 MET cc_start: 0.8611 (pmm) cc_final: 0.8223 (pmm) REVERT: F 380 LYS cc_start: 0.6814 (ttmt) cc_final: 0.6525 (ttpp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2090 time to fit residues: 47.8171 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 : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 78 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 146 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 411 ASN F 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.045119 restraints weight = 87943.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046314 restraints weight = 57776.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047115 restraints weight = 42064.717| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11634 Z= 0.114 Angle : 0.527 11.119 15945 Z= 0.279 Chirality : 0.040 0.129 1966 Planarity : 0.004 0.043 2061 Dihedral : 11.100 88.365 1928 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1612 helix: 0.10 (0.18), residues: 829 sheet: -0.45 (0.38), residues: 192 loop : -0.41 (0.29), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 465 HIS 0.005 0.002 HIS E 206 PHE 0.022 0.001 PHE F 317 TYR 0.033 0.001 TYR F 284 ARG 0.004 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 484) hydrogen bonds : angle 4.37913 ( 1398) covalent geometry : bond 0.00251 (11633) covalent geometry : angle 0.52659 (15945) Misc. bond : bond 0.00016 ( 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 162 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.207 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 207 GLU cc_start: 0.8321 (mp0) cc_final: 0.8062 (pm20) REVERT: A 229 MET cc_start: 0.6340 (pmm) cc_final: 0.5924 (ppp) REVERT: A 372 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8865 (mm-30) REVERT: B 198 MET cc_start: 0.9065 (mpp) cc_final: 0.8747 (mpp) REVERT: B 380 LYS cc_start: 0.9294 (mtmm) cc_final: 0.8996 (tttm) REVERT: C 198 MET cc_start: 0.9106 (mtm) cc_final: 0.8644 (mtm) REVERT: C 207 GLU cc_start: 0.6920 (pt0) cc_final: 0.5676 (pp20) REVERT: C 229 MET cc_start: 0.9217 (ppp) cc_final: 0.9000 (ppp) REVERT: C 254 PHE cc_start: 0.8454 (t80) cc_final: 0.7973 (t80) REVERT: C 371 ILE cc_start: 0.9449 (mt) cc_final: 0.9159 (mm) REVERT: C 376 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8615 (mm-30) REVERT: D 203 GLN cc_start: 0.9501 (tt0) cc_final: 0.8965 (pp30) REVERT: D 207 GLU cc_start: 0.8164 (pt0) cc_final: 0.7877 (pt0) REVERT: D 293 GLN cc_start: 0.7755 (mm110) cc_final: 0.7475 (mm110) REVERT: D 372 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7656 (mp0) REVERT: D 375 MET cc_start: 0.9094 (mmm) cc_final: 0.8154 (tpt) REVERT: E 203 GLN cc_start: 0.8911 (tt0) cc_final: 0.8484 (tp-100) REVERT: E 207 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7014 (pt0) REVERT: F 206 HIS cc_start: 0.8770 (t-90) cc_final: 0.8507 (t-90) REVERT: F 229 MET cc_start: 0.8586 (pmm) cc_final: 0.8113 (pmm) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2019 time to fit residues: 48.8842 Evaluate side-chains 123 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 7 optimal weight: 0.1980 chunk 96 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 411 ASN F 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.057197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045791 restraints weight = 89078.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046842 restraints weight = 58870.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047646 restraints weight = 43149.645| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5305 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= 0.118 Angle : 0.532 12.106 15945 Z= 0.284 Chirality : 0.040 0.166 1966 Planarity : 0.004 0.046 2061 Dihedral : 10.874 85.987 1928 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1612 helix: 0.13 (0.19), residues: 844 sheet: -0.27 (0.38), residues: 192 loop : -0.45 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 465 HIS 0.005 0.001 HIS E 206 PHE 0.017 0.001 PHE E 317 TYR 0.007 0.001 TYR E 386 ARG 0.003 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 484) hydrogen bonds : angle 4.44387 ( 1398) covalent geometry : bond 0.00257 (11633) covalent geometry : angle 0.53212 (15945) Misc. bond : bond 0.00020 ( 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 163 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.422 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: 0.6441 (pmm) cc_final: 0.5994 (ppp) REVERT: A 372 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8813 (mm-30) REVERT: B 198 MET cc_start: 0.9072 (mpp) cc_final: 0.8706 (mpp) REVERT: C 198 MET cc_start: 0.9062 (mtm) cc_final: 0.8791 (mtm) REVERT: C 207 GLU cc_start: 0.7020 (pt0) cc_final: 0.5787 (pp20) REVERT: C 254 PHE cc_start: 0.8496 (t80) cc_final: 0.7987 (t80) REVERT: C 371 ILE cc_start: 0.9405 (mt) cc_final: 0.9122 (mm) REVERT: C 376 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8590 (mm-30) REVERT: D 203 GLN cc_start: 0.9478 (tt0) cc_final: 0.8947 (pp30) REVERT: D 207 GLU cc_start: 0.8166 (pt0) cc_final: 0.7861 (pt0) REVERT: D 293 GLN cc_start: 0.7917 (mm110) cc_final: 0.7628 (mm110) REVERT: D 372 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7653 (mp0) REVERT: D 375 MET cc_start: 0.9071 (mmm) cc_final: 0.8160 (tpt) REVERT: D 383 GLU cc_start: 0.9384 (pt0) cc_final: 0.9142 (pm20) REVERT: E 203 GLN cc_start: 0.8871 (tt0) cc_final: 0.8490 (tp-100) REVERT: E 207 GLU cc_start: 0.7950 (mt-10) cc_final: 0.6990 (pt0) REVERT: E 219 PHE cc_start: 0.9074 (m-80) cc_final: 0.8691 (m-80) REVERT: F 206 HIS cc_start: 0.8742 (t-90) cc_final: 0.8504 (t-90) REVERT: F 229 MET cc_start: 0.8634 (pmm) cc_final: 0.8232 (pmm) REVERT: F 363 ASP cc_start: 0.9381 (m-30) cc_final: 0.8626 (p0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2055 time to fit residues: 50.4015 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 : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 117 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 140 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 411 ASN F 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.057116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045455 restraints weight = 88796.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046588 restraints weight = 58561.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047347 restraints weight = 42644.208| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5516 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= 0.113 Angle : 0.528 12.936 15945 Z= 0.279 Chirality : 0.040 0.143 1966 Planarity : 0.004 0.045 2061 Dihedral : 10.725 86.092 1928 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1612 helix: 0.24 (0.19), residues: 844 sheet: -0.21 (0.38), residues: 192 loop : -0.38 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 465 HIS 0.005 0.001 HIS E 206 PHE 0.015 0.001 PHE E 317 TYR 0.006 0.001 TYR E 284 ARG 0.003 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 484) hydrogen bonds : angle 4.37252 ( 1398) covalent geometry : bond 0.00247 (11633) covalent geometry : angle 0.52758 (15945) Misc. bond : bond 0.00020 ( 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 157 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.357 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 229 MET cc_start: 0.6564 (pmm) cc_final: 0.6048 (ppp) REVERT: A 372 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8833 (mm-30) REVERT: B 198 MET cc_start: 0.8974 (mpp) cc_final: 0.8625 (mpp) REVERT: C 198 MET cc_start: 0.9054 (mtm) cc_final: 0.8756 (mtm) REVERT: C 207 GLU cc_start: 0.7141 (pt0) cc_final: 0.5862 (pp20) REVERT: C 254 PHE cc_start: 0.8515 (t80) cc_final: 0.8017 (t80) REVERT: C 371 ILE cc_start: 0.9412 (mt) cc_final: 0.9136 (mm) REVERT: D 203 GLN cc_start: 0.9466 (tt0) cc_final: 0.8376 (tm-30) REVERT: D 207 GLU cc_start: 0.8167 (pt0) cc_final: 0.6492 (pt0) REVERT: D 293 GLN cc_start: 0.7928 (mm110) cc_final: 0.7669 (mm110) REVERT: D 372 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7809 (mp0) REVERT: D 375 MET cc_start: 0.9078 (mmm) cc_final: 0.8149 (tpt) REVERT: D 383 GLU cc_start: 0.9402 (pt0) cc_final: 0.9147 (pm20) REVERT: E 207 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7622 (pt0) REVERT: E 375 MET cc_start: 0.8639 (mtm) cc_final: 0.7870 (tmm) REVERT: F 206 HIS cc_start: 0.8751 (t-90) cc_final: 0.8550 (t-90) REVERT: F 229 MET cc_start: 0.8813 (pmm) cc_final: 0.8250 (pmm) REVERT: F 363 ASP cc_start: 0.9359 (m-30) cc_final: 0.8641 (p0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2041 time to fit residues: 48.1067 Evaluate side-chains 125 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 148 optimal weight: 0.0370 chunk 59 optimal weight: 0.4980 chunk 27 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.058493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047134 restraints weight = 92523.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048157 restraints weight = 61873.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048907 restraints weight = 45608.000| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11634 Z= 0.131 Angle : 0.549 13.796 15945 Z= 0.288 Chirality : 0.040 0.143 1966 Planarity : 0.004 0.042 2061 Dihedral : 10.689 87.602 1928 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1612 helix: 0.31 (0.19), residues: 844 sheet: -0.18 (0.38), residues: 198 loop : -0.33 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 465 HIS 0.006 0.001 HIS E 206 PHE 0.017 0.001 PHE E 317 TYR 0.008 0.001 TYR A 386 ARG 0.015 0.001 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 484) hydrogen bonds : angle 4.41579 ( 1398) covalent geometry : bond 0.00285 (11633) covalent geometry : angle 0.54852 (15945) Misc. bond : bond 0.00019 ( 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 154 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 2.077 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: 0.6483 (pmm) cc_final: 0.6147 (ppp) REVERT: A 372 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8849 (mm-30) REVERT: B 198 MET cc_start: 0.9038 (mpp) cc_final: 0.8665 (mpp) REVERT: B 375 MET cc_start: 0.8881 (tpp) cc_final: 0.8336 (tpt) REVERT: C 198 MET cc_start: 0.9095 (mtm) cc_final: 0.8836 (mtm) REVERT: C 207 GLU cc_start: 0.7196 (pt0) cc_final: 0.5859 (pp20) REVERT: C 254 PHE cc_start: 0.8618 (t80) cc_final: 0.8068 (t80) REVERT: C 371 ILE cc_start: 0.9410 (mt) cc_final: 0.9154 (mm) REVERT: D 203 GLN cc_start: 0.9485 (tt0) cc_final: 0.8799 (tm-30) REVERT: D 293 GLN cc_start: 0.8065 (mm110) cc_final: 0.7798 (mm110) REVERT: D 372 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7903 (mp0) REVERT: D 375 MET cc_start: 0.9096 (mmm) cc_final: 0.8160 (tpt) REVERT: D 383 GLU cc_start: 0.9385 (pt0) cc_final: 0.9122 (pm20) REVERT: E 207 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7697 (pt0) REVERT: E 375 MET cc_start: 0.8788 (mtm) cc_final: 0.8049 (tmm) REVERT: F 207 GLU cc_start: 0.9149 (pt0) cc_final: 0.8801 (pp20) REVERT: F 229 MET cc_start: 0.8847 (pmm) cc_final: 0.8226 (pmm) REVERT: F 363 ASP cc_start: 0.9397 (m-30) cc_final: 0.8737 (p0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2688 time to fit residues: 64.0870 Evaluate side-chains 123 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 115 optimal weight: 0.3980 chunk 83 optimal weight: 0.4980 chunk 1 optimal weight: 0.0270 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 0.0670 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 ASN E 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.057889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.045901 restraints weight = 86468.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047022 restraints weight = 56927.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.047865 restraints weight = 41488.718| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11634 Z= 0.101 Angle : 0.529 13.665 15945 Z= 0.277 Chirality : 0.040 0.138 1966 Planarity : 0.004 0.060 2061 Dihedral : 10.416 86.911 1928 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1612 helix: 0.46 (0.19), residues: 844 sheet: -0.03 (0.37), residues: 198 loop : -0.36 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 465 HIS 0.005 0.001 HIS E 206 PHE 0.008 0.001 PHE B 353 TYR 0.005 0.001 TYR D 284 ARG 0.014 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 484) hydrogen bonds : angle 4.23617 ( 1398) covalent geometry : bond 0.00219 (11633) covalent geometry : angle 0.52942 (15945) Misc. bond : bond 0.00014 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4361.81 seconds wall clock time: 77 minutes 27.76 seconds (4647.76 seconds total)