Starting phenix.real_space_refine on Sat Aug 23 16:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ohs_16884/08_2025/8ohs_16884.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ohs_16884/08_2025/8ohs_16884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ohs_16884/08_2025/8ohs_16884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ohs_16884/08_2025/8ohs_16884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ohs_16884/08_2025/8ohs_16884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ohs_16884/08_2025/8ohs_16884.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 8487 2.51 5 N 2286 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13335 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "C" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "D" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "E" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "G" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Time building chain proxies: 3.10, per 1000 atoms: 0.23 Number of scatterers: 13335 At special positions: 0 Unit cell: (162.5, 167.5, 116.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 2535 8.00 N 2286 7.00 C 8487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 452.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 27 sheets defined 43.9% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.681A pdb=" N LYS A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.839A pdb=" N PHE A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.835A pdb=" N GLN A 366 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 452 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'C' and resid 275 through 289 Processing helix chain 'C' and resid 294 through 307 removed outlier: 4.198A pdb=" N PHE C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 Processing helix chain 'C' and resid 399 through 419 removed outlier: 4.562A pdb=" N LYS C 403 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 407 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 250 removed outlier: 3.733A pdb=" N LYS B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.844A pdb=" N PHE B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.848A pdb=" N GLN B 366 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'D' and resid 233 through 250 removed outlier: 3.681A pdb=" N LYS D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 282 through 298 removed outlier: 3.839A pdb=" N PHE D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.834A pdb=" N GLN D 366 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 452 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'E' and resid 275 through 289 Processing helix chain 'E' and resid 294 through 307 removed outlier: 4.198A pdb=" N PHE E 298 " --> pdb=" O PRO E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 329 Processing helix chain 'E' and resid 399 through 419 removed outlier: 4.562A pdb=" N LYS E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG E 404 " --> pdb=" O SER E 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 407 " --> pdb=" O LYS E 403 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 removed outlier: 3.733A pdb=" N LYS F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR F 238 " --> pdb=" O GLY F 234 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG F 242 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 272 Processing helix chain 'F' and resid 282 through 298 removed outlier: 3.844A pdb=" N PHE F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 340 through 358 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.848A pdb=" N GLN F 366 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 452 Processing helix chain 'F' and resid 453 through 457 Processing helix chain 'G' and resid 233 through 250 removed outlier: 3.682A pdb=" N LYS G 237 " --> pdb=" O SER G 233 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR G 238 " --> pdb=" O GLY G 234 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 272 Processing helix chain 'G' and resid 282 through 298 removed outlier: 3.839A pdb=" N PHE G 286 " --> pdb=" O SER G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 301 No H-bonds generated for 'chain 'G' and resid 299 through 301' Processing helix chain 'G' and resid 340 through 358 Processing helix chain 'G' and resid 361 through 366 removed outlier: 3.835A pdb=" N GLN G 366 " --> pdb=" O GLU G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 452 Processing helix chain 'G' and resid 453 through 457 Processing helix chain 'H' and resid 275 through 289 Processing helix chain 'H' and resid 294 through 307 removed outlier: 4.199A pdb=" N PHE H 298 " --> pdb=" O PRO H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 329 Processing helix chain 'H' and resid 399 through 419 removed outlier: 4.562A pdb=" N LYS H 403 " --> pdb=" O LYS H 399 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG H 404 " --> pdb=" O SER H 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 407 " --> pdb=" O LYS H 403 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 250 removed outlier: 3.734A pdb=" N LYS I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR I 238 " --> pdb=" O GLY I 234 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG I 242 " --> pdb=" O THR I 238 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 272 Processing helix chain 'I' and resid 282 through 298 removed outlier: 3.844A pdb=" N PHE I 286 " --> pdb=" O SER I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 301 No H-bonds generated for 'chain 'I' and resid 299 through 301' Processing helix chain 'I' and resid 340 through 358 Processing helix chain 'I' and resid 361 through 366 removed outlier: 3.848A pdb=" N GLN I 366 " --> pdb=" O GLU I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 452 Processing helix chain 'I' and resid 453 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 231 Processing sheet with id=AA2, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.474A pdb=" N SER A 319 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN A 374 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER A 371 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 398 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 373 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.474A pdb=" N SER A 319 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN A 374 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER A 371 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 398 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 373 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 383 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA6, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.640A pdb=" N SER A 383 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER G 371 " --> pdb=" O LEU G 396 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL G 398 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER G 373 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER G 319 " --> pdb=" O ILE G 372 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN G 374 " --> pdb=" O SER G 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.640A pdb=" N SER A 383 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR G 414 " --> pdb=" O ASN G 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 266 through 271 Processing sheet with id=AA9, first strand: chain 'B' and resid 252 through 260 removed outlier: 6.564A pdb=" N SER B 371 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL B 398 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER B 373 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER B 319 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN B 374 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 260 removed outlier: 3.697A pdb=" N THR B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 303 through 305 Processing sheet with id=AB3, first strand: chain 'B' and resid 323 through 324 Processing sheet with id=AB4, first strand: chain 'D' and resid 332 through 333 removed outlier: 6.474A pdb=" N SER D 319 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN D 374 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER D 371 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL D 398 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER D 373 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 332 through 333 removed outlier: 6.474A pdb=" N SER D 319 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN D 374 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER D 371 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL D 398 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER D 373 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER G 383 " --> pdb=" O SER D 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 303 through 305 Processing sheet with id=AB7, first strand: chain 'D' and resid 322 through 324 Processing sheet with id=AB8, first strand: chain 'E' and resid 266 through 271 Processing sheet with id=AB9, first strand: chain 'F' and resid 252 through 260 removed outlier: 6.564A pdb=" N SER F 371 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL F 398 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER F 373 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER F 319 " --> pdb=" O ILE F 372 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN F 374 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 252 through 260 removed outlier: 3.698A pdb=" N THR F 414 " --> pdb=" O ASN F 410 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 303 through 305 Processing sheet with id=AC3, first strand: chain 'F' and resid 323 through 324 Processing sheet with id=AC4, first strand: chain 'G' and resid 322 through 324 Processing sheet with id=AC5, first strand: chain 'H' and resid 266 through 271 Processing sheet with id=AC6, first strand: chain 'I' and resid 252 through 260 removed outlier: 6.564A pdb=" N SER I 371 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL I 398 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER I 373 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER I 319 " --> pdb=" O ILE I 372 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN I 374 " --> pdb=" O SER I 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 252 through 260 removed outlier: 3.698A pdb=" N THR I 414 " --> pdb=" O ASN I 410 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 303 through 305 Processing sheet with id=AC9, first strand: chain 'I' and resid 323 through 324 738 hydrogen bonds defined for protein. 2055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3773 1.34 - 1.46: 1766 1.46 - 1.58: 7961 1.58 - 1.70: 3 1.70 - 1.82: 54 Bond restraints: 13557 Sorted by residual: bond pdb=" N VAL A 298 " pdb=" CA VAL A 298 " ideal model delta sigma weight residual 1.456 1.486 -0.030 8.60e-03 1.35e+04 1.20e+01 bond pdb=" N VAL G 298 " pdb=" CA VAL G 298 " ideal model delta sigma weight residual 1.456 1.486 -0.030 8.60e-03 1.35e+04 1.19e+01 bond pdb=" N VAL D 298 " pdb=" CA VAL D 298 " ideal model delta sigma weight residual 1.456 1.485 -0.030 8.60e-03 1.35e+04 1.18e+01 bond pdb=" N ILE D 332 " pdb=" CA ILE D 332 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.14e-02 7.69e+03 1.12e+01 bond pdb=" N ILE G 332 " pdb=" CA ILE G 332 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.14e-02 7.69e+03 1.11e+01 ... (remaining 13552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 15276 1.42 - 2.84: 2680 2.84 - 4.26: 329 4.26 - 5.68: 87 5.68 - 7.10: 18 Bond angle restraints: 18390 Sorted by residual: angle pdb=" CA GLY A 327 " pdb=" C GLY A 327 " pdb=" O GLY A 327 " ideal model delta sigma weight residual 122.56 118.22 4.34 1.03e+00 9.43e-01 1.78e+01 angle pdb=" CA GLY G 327 " pdb=" C GLY G 327 " pdb=" O GLY G 327 " ideal model delta sigma weight residual 122.56 118.22 4.34 1.03e+00 9.43e-01 1.78e+01 angle pdb=" CA GLY D 327 " pdb=" C GLY D 327 " pdb=" O GLY D 327 " ideal model delta sigma weight residual 122.56 118.26 4.30 1.03e+00 9.43e-01 1.74e+01 angle pdb=" N GLU E 417 " pdb=" CA GLU E 417 " pdb=" C GLU E 417 " ideal model delta sigma weight residual 113.88 109.03 4.85 1.23e+00 6.61e-01 1.56e+01 angle pdb=" N GLU C 417 " pdb=" CA GLU C 417 " pdb=" C GLU C 417 " ideal model delta sigma weight residual 113.88 109.03 4.85 1.23e+00 6.61e-01 1.56e+01 ... (remaining 18385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7635 17.88 - 35.75: 513 35.75 - 53.63: 132 53.63 - 71.51: 48 71.51 - 89.38: 24 Dihedral angle restraints: 8352 sinusoidal: 3294 harmonic: 5058 Sorted by residual: dihedral pdb=" CB GLU I 445 " pdb=" CG GLU I 445 " pdb=" CD GLU I 445 " pdb=" OE1 GLU I 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.38 -89.38 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU F 445 " pdb=" CG GLU F 445 " pdb=" CD GLU F 445 " pdb=" OE1 GLU F 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.36 -89.36 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 445 " pdb=" CG GLU B 445 " pdb=" CD GLU B 445 " pdb=" OE1 GLU B 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.35 -89.35 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1303 0.059 - 0.117: 615 0.117 - 0.176: 245 0.176 - 0.235: 30 0.235 - 0.293: 6 Chirality restraints: 2199 Sorted by residual: chirality pdb=" CB THR C 345 " pdb=" CA THR C 345 " pdb=" OG1 THR C 345 " pdb=" CG2 THR C 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB THR E 345 " pdb=" CA THR E 345 " pdb=" OG1 THR E 345 " pdb=" CG2 THR E 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB THR H 345 " pdb=" CA THR H 345 " pdb=" OG1 THR H 345 " pdb=" CG2 THR H 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 2196 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I 348 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C VAL I 348 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL I 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS I 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 348 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C VAL B 348 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL B 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS B 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 348 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C VAL F 348 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL F 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS F 349 " 0.014 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 0.70 - 1.54: 3 1.54 - 2.38: 6 2.38 - 3.22: 11964 3.22 - 4.06: 30116 4.06 - 4.90: 53895 Warning: very small nonbonded interaction distances. Nonbonded interactions: 95984 Sorted by model distance: nonbonded pdb=" O THR E 288 " pdb=" NZ LYS H 284 " model vdw 0.697 3.120 nonbonded pdb=" NZ LYS C 284 " pdb=" O THR H 288 " model vdw 0.700 3.120 nonbonded pdb=" O THR C 288 " pdb=" NZ LYS E 284 " model vdw 0.702 3.120 nonbonded pdb=" NZ LYS C 284 " pdb=" C THR H 288 " model vdw 1.549 3.350 nonbonded pdb=" C THR E 288 " pdb=" NZ LYS H 284 " model vdw 1.554 3.350 ... (remaining 95979 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.780 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.009 0.079 13557 Z= 0.618 Angle : 1.089 7.101 18390 Z= 0.722 Chirality : 0.075 0.293 2199 Planarity : 0.004 0.033 2352 Dihedral : 14.895 89.383 5064 Min Nonbonded Distance : 0.697 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.41 % Allowed : 2.44 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.19), residues: 1734 helix: 0.64 (0.20), residues: 651 sheet: -0.25 (0.28), residues: 285 loop : -2.05 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 268 TYR 0.020 0.003 TYR C 316 PHE 0.017 0.002 PHE E 408 TRP 0.013 0.003 TRP F 442 HIS 0.006 0.002 HIS I 252 Details of bonding type rmsd covalent geometry : bond 0.00900 (13557) covalent geometry : angle 1.08853 (18390) hydrogen bonds : bond 0.15285 ( 693) hydrogen bonds : angle 6.35802 ( 2055) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 422 time to evaluate : 0.494 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: C 415 VAL cc_start: 0.7321 (t) cc_final: 0.7032 (m) REVERT: B 236 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.5155 (tmt170) REVERT: B 382 GLN cc_start: 0.8370 (tt0) cc_final: 0.6662 (pm20) REVERT: B 396 LEU cc_start: 0.9509 (tp) cc_final: 0.9166 (tt) REVERT: D 229 ASP cc_start: 0.7620 (m-30) cc_final: 0.7146 (m-30) REVERT: E 300 THR cc_start: 0.7239 (p) cc_final: 0.6950 (t) REVERT: F 236 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.5409 (tmt170) REVERT: F 382 GLN cc_start: 0.8261 (tt0) cc_final: 0.6533 (pm20) REVERT: G 421 GLU cc_start: 0.7612 (tt0) cc_final: 0.7401 (tt0) REVERT: H 300 THR cc_start: 0.7433 (p) cc_final: 0.7108 (t) REVERT: I 236 ARG cc_start: 0.7175 (ttm-80) cc_final: 0.5162 (tmt170) REVERT: I 382 GLN cc_start: 0.8356 (tt0) cc_final: 0.6380 (pm20) outliers start: 6 outliers final: 0 residues processed: 422 average time/residue: 0.1274 time to fit residues: 72.2439 Evaluate side-chains 181 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 382 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN C 410 GLN B 389 ASN D 312 GLN D 378 ASN F 389 ASN G 312 GLN G 378 ASN H 317 GLN I 389 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.073348 restraints weight = 35339.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.072550 restraints weight = 32319.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.072729 restraints weight = 27916.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073004 restraints weight = 26636.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073259 restraints weight = 24464.731| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13557 Z= 0.123 Angle : 0.583 7.073 18390 Z= 0.296 Chirality : 0.044 0.151 2199 Planarity : 0.004 0.039 2352 Dihedral : 3.956 17.704 1836 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.20), residues: 1734 helix: 2.21 (0.21), residues: 675 sheet: 0.04 (0.26), residues: 273 loop : -1.70 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 242 TYR 0.032 0.003 TYR B 365 PHE 0.016 0.002 PHE G 253 TRP 0.010 0.002 TRP A 419 HIS 0.002 0.001 HIS I 252 Details of bonding type rmsd covalent geometry : bond 0.00284 (13557) covalent geometry : angle 0.58348 (18390) hydrogen bonds : bond 0.03268 ( 693) hydrogen bonds : angle 3.99732 ( 2055) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.464 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: B 236 ARG cc_start: 0.7825 (tpp-160) cc_final: 0.5329 (tmt170) REVERT: D 229 ASP cc_start: 0.8056 (m-30) cc_final: 0.7610 (m-30) REVERT: D 357 ASP cc_start: 0.8012 (m-30) cc_final: 0.7677 (m-30) REVERT: E 300 THR cc_start: 0.8536 (p) cc_final: 0.8220 (p) REVERT: E 408 PHE cc_start: 0.5417 (t80) cc_final: 0.4740 (t80) REVERT: F 236 ARG cc_start: 0.7747 (tpp-160) cc_final: 0.5457 (tmt170) REVERT: H 300 THR cc_start: 0.8603 (p) cc_final: 0.8338 (p) REVERT: H 326 GLN cc_start: 0.9027 (mt0) cc_final: 0.8806 (mm-40) REVERT: I 236 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.5574 (tmt170) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1470 time to fit residues: 47.7248 Evaluate side-chains 150 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 169 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 134 optimal weight: 0.0570 chunk 71 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.2280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 382 GLN A 389 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN C 410 GLN B 402 GLN D 284 ASN D 378 ASN ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN I 284 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.095587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.070559 restraints weight = 35626.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070048 restraints weight = 33376.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.070553 restraints weight = 31485.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.070884 restraints weight = 26564.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.070948 restraints weight = 24182.326| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13557 Z= 0.109 Angle : 0.532 8.158 18390 Z= 0.270 Chirality : 0.043 0.141 2199 Planarity : 0.004 0.042 2352 Dihedral : 3.738 20.510 1836 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.20), residues: 1734 helix: 2.43 (0.21), residues: 681 sheet: 0.55 (0.25), residues: 285 loop : -1.28 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 242 TYR 0.034 0.002 TYR F 365 PHE 0.022 0.001 PHE G 253 TRP 0.008 0.001 TRP A 419 HIS 0.005 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00249 (13557) covalent geometry : angle 0.53217 (18390) hydrogen bonds : bond 0.02927 ( 693) hydrogen bonds : angle 3.65549 ( 2055) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.6340 (tpt) cc_final: 0.5746 (tpp) REVERT: B 236 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.5402 (tmt170) REVERT: E 300 THR cc_start: 0.8391 (p) cc_final: 0.8134 (p) REVERT: E 408 PHE cc_start: 0.5228 (t80) cc_final: 0.4955 (t80) REVERT: F 236 ARG cc_start: 0.7693 (tpp-160) cc_final: 0.5638 (tmt170) REVERT: F 350 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7573 (tm-30) REVERT: H 300 THR cc_start: 0.8724 (p) cc_final: 0.8382 (p) REVERT: I 236 ARG cc_start: 0.7829 (tpp-160) cc_final: 0.5620 (tmt170) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1482 time to fit residues: 39.0982 Evaluate side-chains 145 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 33 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 114 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 378 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN B 252 HIS D 378 ASN F 284 ASN G 378 ASN G 389 ASN H 282 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.068954 restraints weight = 35892.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.068396 restraints weight = 35998.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.068896 restraints weight = 32319.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.069248 restraints weight = 27441.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.069280 restraints weight = 25801.005| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13557 Z= 0.120 Angle : 0.527 6.183 18390 Z= 0.267 Chirality : 0.043 0.133 2199 Planarity : 0.004 0.043 2352 Dihedral : 3.723 17.711 1836 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.21), residues: 1734 helix: 2.52 (0.21), residues: 687 sheet: 0.75 (0.25), residues: 285 loop : -1.07 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 339 TYR 0.024 0.002 TYR B 365 PHE 0.019 0.001 PHE G 253 TRP 0.008 0.001 TRP A 419 HIS 0.001 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00282 (13557) covalent geometry : angle 0.52733 (18390) hydrogen bonds : bond 0.02844 ( 693) hydrogen bonds : angle 3.53153 ( 2055) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.6419 (tpt) cc_final: 0.5709 (tpp) REVERT: B 236 ARG cc_start: 0.7876 (tpp-160) cc_final: 0.5694 (ttt180) REVERT: D 229 ASP cc_start: 0.7980 (m-30) cc_final: 0.7545 (m-30) REVERT: E 408 PHE cc_start: 0.5244 (t80) cc_final: 0.4687 (t80) REVERT: F 236 ARG cc_start: 0.7773 (tpp-160) cc_final: 0.5888 (tmt170) REVERT: H 300 THR cc_start: 0.8603 (p) cc_final: 0.8140 (t) REVERT: I 236 ARG cc_start: 0.7918 (tpp-160) cc_final: 0.5801 (tmt170) REVERT: I 253 PHE cc_start: 0.8820 (p90) cc_final: 0.8597 (p90) REVERT: I 291 MET cc_start: 0.8574 (ttm) cc_final: 0.8229 (ttm) REVERT: I 444 ARG cc_start: 0.4910 (mtt-85) cc_final: 0.4199 (mtt180) outliers start: 1 outliers final: 1 residues processed: 195 average time/residue: 0.1557 time to fit residues: 39.9880 Evaluate side-chains 144 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 172 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 0.0870 chunk 86 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 326 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN D 378 ASN E 326 GLN G 378 ASN H 410 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.070044 restraints weight = 35599.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.069097 restraints weight = 35342.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.069755 restraints weight = 32157.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.070120 restraints weight = 27023.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.070174 restraints weight = 25168.430| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13557 Z= 0.092 Angle : 0.503 6.029 18390 Z= 0.254 Chirality : 0.042 0.139 2199 Planarity : 0.004 0.045 2352 Dihedral : 3.594 17.548 1836 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.07 % Allowed : 1.77 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.21), residues: 1734 helix: 2.60 (0.21), residues: 687 sheet: 0.67 (0.25), residues: 321 loop : -0.82 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 242 TYR 0.031 0.002 TYR F 365 PHE 0.016 0.001 PHE G 253 TRP 0.006 0.001 TRP D 419 HIS 0.002 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00212 (13557) covalent geometry : angle 0.50264 (18390) hydrogen bonds : bond 0.02529 ( 693) hydrogen bonds : angle 3.30848 ( 2055) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7986 (m-30) cc_final: 0.7474 (m-30) REVERT: A 357 ASP cc_start: 0.8205 (m-30) cc_final: 0.7572 (m-30) REVERT: B 235 MET cc_start: 0.6431 (tpt) cc_final: 0.5791 (tpp) REVERT: B 236 ARG cc_start: 0.7786 (tpp-160) cc_final: 0.5709 (tmt170) REVERT: B 382 GLN cc_start: 0.8760 (tt0) cc_final: 0.6977 (pm20) REVERT: D 229 ASP cc_start: 0.7966 (m-30) cc_final: 0.7540 (m-30) REVERT: E 397 VAL cc_start: 0.6191 (t) cc_final: 0.5934 (p) REVERT: E 408 PHE cc_start: 0.5496 (t80) cc_final: 0.4824 (t80) REVERT: F 236 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.5927 (tmt170) REVERT: F 382 GLN cc_start: 0.8736 (tt0) cc_final: 0.6447 (pm20) REVERT: H 300 THR cc_start: 0.8676 (p) cc_final: 0.8298 (p) REVERT: I 236 ARG cc_start: 0.7803 (tpp-160) cc_final: 0.5779 (tmt170) REVERT: I 382 GLN cc_start: 0.8790 (tt0) cc_final: 0.6868 (pm20) REVERT: I 444 ARG cc_start: 0.4907 (mtt-85) cc_final: 0.4180 (mtt180) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1501 time to fit residues: 39.8705 Evaluate side-chains 140 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 0.4980 chunk 92 optimal weight: 10.0000 chunk 169 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 326 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN B 252 HIS D 378 ASN E 286 HIS E 410 GLN G 378 ASN H 282 GLN H 410 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.092311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.067959 restraints weight = 35349.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.067254 restraints weight = 37067.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.067826 restraints weight = 32778.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.068171 restraints weight = 27675.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.068212 restraints weight = 25896.862| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13557 Z= 0.127 Angle : 0.534 14.260 18390 Z= 0.274 Chirality : 0.042 0.132 2199 Planarity : 0.004 0.045 2352 Dihedral : 3.692 19.518 1836 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.14 % Allowed : 3.05 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.21), residues: 1734 helix: 2.65 (0.21), residues: 687 sheet: 0.65 (0.25), residues: 321 loop : -0.67 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 339 TYR 0.015 0.002 TYR H 316 PHE 0.019 0.002 PHE G 253 TRP 0.007 0.001 TRP A 442 HIS 0.008 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00298 (13557) covalent geometry : angle 0.53447 (18390) hydrogen bonds : bond 0.02974 ( 693) hydrogen bonds : angle 3.46050 ( 2055) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.6299 (tpt) cc_final: 0.5983 (tpp) REVERT: B 236 ARG cc_start: 0.7923 (tpp-160) cc_final: 0.6015 (ttt180) REVERT: B 382 GLN cc_start: 0.8774 (tt0) cc_final: 0.7080 (pm20) REVERT: D 229 ASP cc_start: 0.8055 (m-30) cc_final: 0.7746 (m-30) REVERT: F 236 ARG cc_start: 0.7890 (tpp-160) cc_final: 0.6062 (tmt170) REVERT: F 382 GLN cc_start: 0.8718 (tt0) cc_final: 0.6364 (pm20) REVERT: F 444 ARG cc_start: 0.4613 (mtt-85) cc_final: 0.3866 (mtt180) REVERT: H 300 THR cc_start: 0.8788 (p) cc_final: 0.8523 (p) REVERT: I 236 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.5980 (tmt170) REVERT: I 253 PHE cc_start: 0.8861 (p90) cc_final: 0.8388 (p90) REVERT: I 382 GLN cc_start: 0.8788 (tt0) cc_final: 0.6952 (pm20) REVERT: I 444 ARG cc_start: 0.5003 (mtt-85) cc_final: 0.4255 (mtt180) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.1418 time to fit residues: 35.7504 Evaluate side-chains 149 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 112 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 9 optimal weight: 0.0270 chunk 95 optimal weight: 6.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS C 410 GLN B 431 HIS D 312 GLN D 378 ASN G 326 ASN H 286 HIS H 326 GLN H 410 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.088742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.063583 restraints weight = 35624.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.063055 restraints weight = 30335.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.063037 restraints weight = 30808.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.063450 restraints weight = 27407.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.063533 restraints weight = 25065.742| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13557 Z= 0.167 Angle : 0.586 12.957 18390 Z= 0.301 Chirality : 0.043 0.136 2199 Planarity : 0.004 0.046 2352 Dihedral : 4.006 23.539 1836 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.14 % Allowed : 2.17 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.21), residues: 1734 helix: 2.54 (0.21), residues: 675 sheet: 0.62 (0.25), residues: 321 loop : -0.68 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 242 TYR 0.013 0.002 TYR B 365 PHE 0.027 0.002 PHE G 253 TRP 0.009 0.001 TRP A 442 HIS 0.008 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00398 (13557) covalent geometry : angle 0.58634 (18390) hydrogen bonds : bond 0.03256 ( 693) hydrogen bonds : angle 3.69298 ( 2055) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.399 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: B 227 TYR cc_start: 0.2395 (t80) cc_final: 0.2185 (t80) REVERT: B 236 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.5925 (tmt170) REVERT: B 242 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7975 (ttm110) REVERT: B 377 MET cc_start: 0.8268 (mpp) cc_final: 0.8045 (mpp) REVERT: B 434 VAL cc_start: 0.9530 (t) cc_final: 0.9327 (m) REVERT: D 229 ASP cc_start: 0.8240 (m-30) cc_final: 0.7865 (m-30) REVERT: E 408 PHE cc_start: 0.6347 (t80) cc_final: 0.5834 (t80) REVERT: F 236 ARG cc_start: 0.7947 (tpp-160) cc_final: 0.6114 (tmt170) REVERT: F 444 ARG cc_start: 0.4615 (mtt-85) cc_final: 0.4214 (mtt90) REVERT: H 296 SER cc_start: 0.7915 (t) cc_final: 0.7391 (p) REVERT: I 227 TYR cc_start: 0.6757 (p90) cc_final: 0.6477 (t80) REVERT: I 236 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.6096 (tmt170) REVERT: I 382 GLN cc_start: 0.8765 (tt0) cc_final: 0.6915 (pm20) REVERT: I 444 ARG cc_start: 0.5204 (mtt-85) cc_final: 0.4442 (mtt180) outliers start: 2 outliers final: 0 residues processed: 189 average time/residue: 0.1562 time to fit residues: 38.3181 Evaluate side-chains 145 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 72 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 127 optimal weight: 0.0040 chunk 89 optimal weight: 9.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN C 410 GLN D 326 ASN G 389 ASN H 282 GLN H 410 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.089010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.063952 restraints weight = 35292.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.063232 restraints weight = 30497.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.063407 restraints weight = 28519.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.063812 restraints weight = 26787.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.063869 restraints weight = 24884.190| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13557 Z= 0.137 Angle : 0.556 12.993 18390 Z= 0.285 Chirality : 0.043 0.140 2199 Planarity : 0.004 0.047 2352 Dihedral : 3.918 20.189 1836 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.14 % Allowed : 0.88 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.21), residues: 1734 helix: 2.50 (0.21), residues: 675 sheet: 0.63 (0.26), residues: 321 loop : -0.69 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 339 TYR 0.012 0.002 TYR B 365 PHE 0.021 0.002 PHE F 253 TRP 0.007 0.001 TRP G 419 HIS 0.004 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00325 (13557) covalent geometry : angle 0.55627 (18390) hydrogen bonds : bond 0.03127 ( 693) hydrogen bonds : angle 3.60979 ( 2055) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.501 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: B 236 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.5915 (tmt170) REVERT: B 242 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7982 (ttm110) REVERT: B 434 VAL cc_start: 0.9480 (t) cc_final: 0.9251 (m) REVERT: D 229 ASP cc_start: 0.8207 (m-30) cc_final: 0.7827 (m-30) REVERT: F 236 ARG cc_start: 0.7826 (tpp-160) cc_final: 0.6096 (tmt170) REVERT: F 242 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8380 (ttm110) REVERT: F 444 ARG cc_start: 0.4697 (mtt-85) cc_final: 0.4279 (mtt90) REVERT: H 296 SER cc_start: 0.7589 (t) cc_final: 0.7370 (p) REVERT: I 227 TYR cc_start: 0.6800 (p90) cc_final: 0.6192 (t80) REVERT: I 236 ARG cc_start: 0.7871 (tpp-160) cc_final: 0.6111 (tmt170) REVERT: I 356 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8172 (mtm-85) REVERT: I 382 GLN cc_start: 0.8749 (tt0) cc_final: 0.6935 (pm20) REVERT: I 444 ARG cc_start: 0.5140 (mtt-85) cc_final: 0.4583 (mtt180) outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 0.1524 time to fit residues: 36.9690 Evaluate side-chains 152 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 13 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 0.0060 chunk 24 optimal weight: 2.9990 overall best weight: 3.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN D 326 ASN E 282 GLN E 410 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.087424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.062240 restraints weight = 35966.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.062026 restraints weight = 31604.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.062708 restraints weight = 27921.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.062692 restraints weight = 23643.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.062772 restraints weight = 24328.263| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13557 Z= 0.190 Angle : 0.619 15.163 18390 Z= 0.316 Chirality : 0.044 0.152 2199 Planarity : 0.005 0.086 2352 Dihedral : 4.218 21.518 1836 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.07 % Allowed : 0.75 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.20), residues: 1734 helix: 2.24 (0.20), residues: 675 sheet: 0.61 (0.26), residues: 321 loop : -0.71 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 339 TYR 0.020 0.002 TYR H 316 PHE 0.026 0.002 PHE E 408 TRP 0.008 0.001 TRP A 419 HIS 0.004 0.001 HIS I 431 Details of bonding type rmsd covalent geometry : bond 0.00450 (13557) covalent geometry : angle 0.61920 (18390) hydrogen bonds : bond 0.03507 ( 693) hydrogen bonds : angle 3.82391 ( 2055) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.355 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: B 236 ARG cc_start: 0.8006 (tpp-160) cc_final: 0.6133 (tmt170) REVERT: B 242 ARG cc_start: 0.8258 (ttm110) cc_final: 0.7938 (ttm110) REVERT: B 377 MET cc_start: 0.8403 (mpp) cc_final: 0.7980 (mpp) REVERT: B 434 VAL cc_start: 0.9508 (t) cc_final: 0.9292 (m) REVERT: D 229 ASP cc_start: 0.8218 (m-30) cc_final: 0.7873 (m-30) REVERT: D 396 LEU cc_start: 0.9610 (tp) cc_final: 0.9400 (tt) REVERT: E 397 VAL cc_start: 0.6232 (t) cc_final: 0.5979 (t) REVERT: E 402 GLU cc_start: 0.7580 (tp30) cc_final: 0.6847 (mm-30) REVERT: E 408 PHE cc_start: 0.6140 (t80) cc_final: 0.5874 (t80) REVERT: F 236 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.6278 (ttt180) REVERT: F 242 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8497 (ttm110) REVERT: F 444 ARG cc_start: 0.4778 (mtt-85) cc_final: 0.4386 (mtt90) REVERT: H 298 PHE cc_start: 0.7461 (m-80) cc_final: 0.6943 (m-80) REVERT: I 227 TYR cc_start: 0.7050 (p90) cc_final: 0.6188 (t80) REVERT: I 236 ARG cc_start: 0.8029 (tpp-160) cc_final: 0.6296 (tmt170) REVERT: I 382 GLN cc_start: 0.8732 (tt0) cc_final: 0.6892 (pm20) REVERT: I 444 ARG cc_start: 0.5145 (mtt-85) cc_final: 0.4588 (mtt180) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1534 time to fit residues: 37.5570 Evaluate side-chains 160 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 3 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 ASN E 282 GLN ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.086322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.062179 restraints weight = 35844.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.061284 restraints weight = 28844.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.061274 restraints weight = 31064.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.061541 restraints weight = 28706.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.061619 restraints weight = 26668.778| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13557 Z= 0.214 Angle : 0.649 14.135 18390 Z= 0.332 Chirality : 0.045 0.181 2199 Planarity : 0.005 0.056 2352 Dihedral : 4.428 21.910 1836 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.20), residues: 1734 helix: 2.12 (0.20), residues: 675 sheet: 0.49 (0.26), residues: 321 loop : -0.84 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 356 TYR 0.015 0.002 TYR A 227 PHE 0.029 0.002 PHE E 408 TRP 0.010 0.001 TRP D 305 HIS 0.003 0.001 HIS I 431 Details of bonding type rmsd covalent geometry : bond 0.00511 (13557) covalent geometry : angle 0.64929 (18390) hydrogen bonds : bond 0.03603 ( 693) hydrogen bonds : angle 3.89137 ( 2055) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.6681 (tpt) cc_final: 0.6308 (tpp) REVERT: B 236 ARG cc_start: 0.7827 (tpp-160) cc_final: 0.6068 (tmt170) REVERT: B 377 MET cc_start: 0.8422 (mpp) cc_final: 0.7976 (mpp) REVERT: B 434 VAL cc_start: 0.9510 (t) cc_final: 0.9293 (m) REVERT: D 229 ASP cc_start: 0.8208 (m-30) cc_final: 0.7875 (m-30) REVERT: E 397 VAL cc_start: 0.6369 (t) cc_final: 0.5981 (t) REVERT: E 402 GLU cc_start: 0.7616 (tp30) cc_final: 0.6896 (mm-30) REVERT: F 236 ARG cc_start: 0.7932 (tpp-160) cc_final: 0.6448 (ttt180) REVERT: F 242 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8532 (ttm110) REVERT: F 444 ARG cc_start: 0.4675 (mtt-85) cc_final: 0.4215 (mtt180) REVERT: H 282 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.6429 (tp40) REVERT: H 298 PHE cc_start: 0.7441 (m-80) cc_final: 0.7088 (m-80) REVERT: I 227 TYR cc_start: 0.7166 (p90) cc_final: 0.6089 (t80) REVERT: I 236 ARG cc_start: 0.8011 (tpp-160) cc_final: 0.6280 (tmt170) REVERT: I 444 ARG cc_start: 0.5212 (mtt-85) cc_final: 0.4665 (mtt180) outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 0.1535 time to fit residues: 37.7305 Evaluate side-chains 168 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 166 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 169 optimal weight: 0.0370 chunk 135 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 150 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN D 326 ASN E 282 GLN E 406 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.063876 restraints weight = 35822.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.063059 restraints weight = 29137.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.063670 restraints weight = 26793.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.063867 restraints weight = 24933.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.063879 restraints weight = 22248.486| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13557 Z= 0.110 Angle : 0.588 14.417 18390 Z= 0.298 Chirality : 0.043 0.199 2199 Planarity : 0.005 0.068 2352 Dihedral : 4.086 20.319 1836 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.07 % Allowed : 0.34 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.21), residues: 1734 helix: 2.43 (0.21), residues: 675 sheet: 0.64 (0.27), residues: 321 loop : -0.71 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 242 TYR 0.012 0.001 TYR B 365 PHE 0.018 0.002 PHE F 253 TRP 0.010 0.001 TRP G 419 HIS 0.002 0.001 HIS I 431 Details of bonding type rmsd covalent geometry : bond 0.00259 (13557) covalent geometry : angle 0.58798 (18390) hydrogen bonds : bond 0.02862 ( 693) hydrogen bonds : angle 3.53520 ( 2055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1846.99 seconds wall clock time: 32 minutes 40.35 seconds (1960.35 seconds total)