Starting phenix.real_space_refine on Thu May 15 14:22:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ohs_16884/05_2025/8ohs_16884.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ohs_16884/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ohs_16884/05_2025/8ohs_16884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ohs_16884/05_2025/8ohs_16884.map" model { file = "/net/cci-nas-00/data/ceres_data/8ohs_16884/05_2025/8ohs_16884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ohs_16884/05_2025/8ohs_16884.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.91, per 1000 atoms: 0.59 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: 3.13 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.77 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: 3.83 Time building geometry restraints manager: 3.66 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: 0.02 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.340 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (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 TRP 0.013 0.003 TRP F 442 HIS 0.006 0.002 HIS I 252 PHE 0.017 0.002 PHE E 408 TYR 0.020 0.003 TYR C 316 ARG 0.003 0.001 ARG D 268 Details of bonding type rmsd hydrogen bonds : bond 0.15285 ( 693) hydrogen bonds : angle 6.35802 ( 2055) covalent geometry : bond 0.00900 (13557) covalent geometry : angle 1.08853 (18390) *********************** 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 : 1.544 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: 0.3254 time to fit residues: 182.9834 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 : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 D 378 ASN F 250 ASN G 312 GLN G 378 ASN H 317 GLN I 250 ASN I 389 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.067812 restraints weight = 35495.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.067132 restraints weight = 33517.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.067677 restraints weight = 31053.447| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13557 Z= 0.189 Angle : 0.639 7.093 18390 Z= 0.326 Chirality : 0.045 0.151 2199 Planarity : 0.004 0.038 2352 Dihedral : 4.238 20.832 1836 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1734 helix: 2.03 (0.21), residues: 681 sheet: 0.18 (0.26), residues: 285 loop : -1.57 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 419 HIS 0.003 0.001 HIS B 252 PHE 0.017 0.002 PHE G 253 TYR 0.032 0.003 TYR B 365 ARG 0.007 0.001 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 693) hydrogen bonds : angle 4.13436 ( 2055) covalent geometry : bond 0.00427 (13557) covalent geometry : angle 0.63899 (18390) *********************** 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 218 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 ARG cc_start: 0.7876 (tpp-160) cc_final: 0.5411 (tmt170) REVERT: B 350 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 365 TYR cc_start: 0.7674 (p90) cc_final: 0.7448 (p90) REVERT: D 229 ASP cc_start: 0.8242 (m-30) cc_final: 0.7872 (m-30) REVERT: D 357 ASP cc_start: 0.8094 (m-30) cc_final: 0.7766 (m-30) REVERT: E 408 PHE cc_start: 0.5415 (t80) cc_final: 0.4728 (t80) REVERT: F 236 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.5770 (tmt170) REVERT: F 253 PHE cc_start: 0.8861 (p90) cc_final: 0.8486 (p90) REVERT: F 365 TYR cc_start: 0.7812 (p90) cc_final: 0.7596 (p90) REVERT: F 444 ARG cc_start: 0.4623 (mtt-85) cc_final: 0.4294 (mtt90) REVERT: H 300 THR cc_start: 0.8577 (p) cc_final: 0.8307 (p) REVERT: H 326 GLN cc_start: 0.9089 (mt0) cc_final: 0.8836 (mm-40) REVERT: I 236 ARG cc_start: 0.7996 (tpp-160) cc_final: 0.5616 (tmt170) REVERT: I 253 PHE cc_start: 0.8924 (p90) cc_final: 0.8557 (p90) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3575 time to fit residues: 102.1462 Evaluate side-chains 146 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 165 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 158 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 252 HIS B 389 ASN D 284 ASN D 378 ASN F 250 ASN F 389 ASN G 312 GLN G 378 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.087119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.061968 restraints weight = 36063.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.061420 restraints weight = 30855.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.061315 restraints weight = 33373.276| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 13557 Z= 0.220 Angle : 0.629 6.196 18390 Z= 0.319 Chirality : 0.045 0.146 2199 Planarity : 0.005 0.044 2352 Dihedral : 4.345 22.047 1836 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1734 helix: 2.20 (0.20), residues: 681 sheet: 0.28 (0.25), residues: 285 loop : -1.35 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 305 HIS 0.007 0.001 HIS C 286 PHE 0.024 0.002 PHE A 253 TYR 0.023 0.003 TYR B 365 ARG 0.007 0.001 ARG F 242 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 693) hydrogen bonds : angle 4.12603 ( 2055) covalent geometry : bond 0.00521 (13557) covalent geometry : angle 0.62855 (18390) *********************** 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 207 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7339 (tm-30) REVERT: C 296 SER cc_start: 0.7253 (t) cc_final: 0.6919 (p) REVERT: B 227 TYR cc_start: 0.6391 (p90) cc_final: 0.5925 (t80) REVERT: B 236 ARG cc_start: 0.8017 (tpp-160) cc_final: 0.6091 (ttt180) REVERT: D 229 ASP cc_start: 0.8053 (m-30) cc_final: 0.7741 (m-30) REVERT: E 300 THR cc_start: 0.8532 (p) cc_final: 0.7928 (p) REVERT: E 408 PHE cc_start: 0.5572 (t80) cc_final: 0.5171 (t80) REVERT: F 227 TYR cc_start: 0.6678 (p90) cc_final: 0.5993 (t80) REVERT: F 236 ARG cc_start: 0.7975 (tpp-160) cc_final: 0.6120 (ttt180) REVERT: F 375 MET cc_start: 0.8454 (mtp) cc_final: 0.8207 (mtt) REVERT: H 308 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7987 (tp40) REVERT: H 326 GLN cc_start: 0.9187 (mt0) cc_final: 0.8876 (mm-40) REVERT: H 406 GLN cc_start: 0.8327 (mt0) cc_final: 0.7902 (mp10) REVERT: H 408 PHE cc_start: 0.5467 (t80) cc_final: 0.5131 (t80) REVERT: I 227 TYR cc_start: 0.6340 (p90) cc_final: 0.6122 (t80) REVERT: I 236 ARG cc_start: 0.8068 (tpp-160) cc_final: 0.6130 (tmt170) REVERT: I 382 GLN cc_start: 0.8807 (tt0) cc_final: 0.7083 (pm20) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.3534 time to fit residues: 96.5240 Evaluate side-chains 155 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 111 optimal weight: 0.0000 chunk 140 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN G 269 GLN G 378 ASN G 389 ASN ** H 282 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 = 0.3388 r_free = 0.3388 target = 0.089600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.062890 restraints weight = 35163.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.063915 restraints weight = 26393.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.064558 restraints weight = 21923.408| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13557 Z= 0.112 Angle : 0.528 6.031 18390 Z= 0.268 Chirality : 0.043 0.139 2199 Planarity : 0.004 0.043 2352 Dihedral : 3.918 17.326 1836 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.14 % Allowed : 2.85 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.21), residues: 1734 helix: 2.50 (0.21), residues: 681 sheet: 0.40 (0.25), residues: 321 loop : -1.02 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 419 HIS 0.002 0.001 HIS D 252 PHE 0.019 0.002 PHE G 253 TYR 0.017 0.002 TYR G 365 ARG 0.008 0.001 ARG I 242 Details of bonding type rmsd hydrogen bonds : bond 0.02821 ( 693) hydrogen bonds : angle 3.58714 ( 2055) covalent geometry : bond 0.00261 (13557) covalent geometry : angle 0.52757 (18390) *********************** 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 205 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7346 (tm-30) REVERT: C 296 SER cc_start: 0.7710 (t) cc_final: 0.7396 (p) REVERT: C 411 LYS cc_start: 0.9273 (mmmm) cc_final: 0.9044 (mttm) REVERT: C 412 MET cc_start: 0.7404 (ptp) cc_final: 0.7197 (ptt) REVERT: B 227 TYR cc_start: 0.6155 (p90) cc_final: 0.5758 (t80) REVERT: B 236 ARG cc_start: 0.7952 (tpp-160) cc_final: 0.6060 (tmt170) REVERT: B 350 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7686 (tm-30) REVERT: D 229 ASP cc_start: 0.8086 (m-30) cc_final: 0.7636 (m-30) REVERT: E 296 SER cc_start: 0.7810 (t) cc_final: 0.7279 (p) REVERT: E 336 LYS cc_start: 0.6844 (mmmt) cc_final: 0.6521 (mmmt) REVERT: E 408 PHE cc_start: 0.5883 (t80) cc_final: 0.5523 (t80) REVERT: F 227 TYR cc_start: 0.6397 (p90) cc_final: 0.5950 (t80) REVERT: F 236 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.6146 (ttt180) REVERT: F 375 MET cc_start: 0.8431 (mtp) cc_final: 0.8217 (mtt) REVERT: F 382 GLN cc_start: 0.8759 (tt0) cc_final: 0.6691 (pm20) REVERT: H 406 GLN cc_start: 0.8348 (mt0) cc_final: 0.8056 (mp10) REVERT: I 227 TYR cc_start: 0.6445 (p90) cc_final: 0.6184 (t80) REVERT: I 236 ARG cc_start: 0.7833 (tpp-160) cc_final: 0.6173 (tmt170) REVERT: I 382 GLN cc_start: 0.8753 (tt0) cc_final: 0.7094 (pm20) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.3786 time to fit residues: 100.1524 Evaluate side-chains 156 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 286 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.062208 restraints weight = 35485.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.063310 restraints weight = 25962.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.063845 restraints weight = 21211.645| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13557 Z= 0.116 Angle : 0.519 6.018 18390 Z= 0.262 Chirality : 0.042 0.140 2199 Planarity : 0.004 0.046 2352 Dihedral : 3.816 17.890 1836 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1734 helix: 2.66 (0.21), residues: 675 sheet: 0.38 (0.25), residues: 327 loop : -0.91 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 419 HIS 0.007 0.001 HIS F 431 PHE 0.015 0.002 PHE E 408 TYR 0.014 0.002 TYR B 365 ARG 0.009 0.001 ARG I 242 Details of bonding type rmsd hydrogen bonds : bond 0.02768 ( 693) hydrogen bonds : angle 3.45156 ( 2055) covalent geometry : bond 0.00278 (13557) covalent geometry : angle 0.51876 (18390) *********************** 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 197 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.8222 (p0) cc_final: 0.8019 (p0) REVERT: A 357 ASP cc_start: 0.8320 (m-30) cc_final: 0.7597 (m-30) REVERT: C 296 SER cc_start: 0.7641 (t) cc_final: 0.7360 (p) REVERT: B 227 TYR cc_start: 0.6463 (p90) cc_final: 0.5559 (t80) REVERT: B 236 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.5925 (tmt170) REVERT: B 350 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7630 (tm-30) REVERT: B 377 MET cc_start: 0.8271 (mpp) cc_final: 0.8061 (mpp) REVERT: D 229 ASP cc_start: 0.8039 (m-30) cc_final: 0.7675 (m-30) REVERT: E 296 SER cc_start: 0.7740 (t) cc_final: 0.7516 (p) REVERT: F 227 TYR cc_start: 0.6574 (p90) cc_final: 0.5905 (t80) REVERT: F 236 ARG cc_start: 0.7926 (tpp-160) cc_final: 0.6193 (ttt180) REVERT: F 382 GLN cc_start: 0.8840 (tt0) cc_final: 0.6846 (pm20) REVERT: F 444 ARG cc_start: 0.4489 (mtt-85) cc_final: 0.4003 (mtt90) REVERT: I 227 TYR cc_start: 0.6670 (p90) cc_final: 0.6224 (t80) REVERT: I 236 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.6200 (tmt170) REVERT: I 382 GLN cc_start: 0.8762 (tt0) cc_final: 0.7095 (pm20) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3554 time to fit residues: 91.3413 Evaluate side-chains 158 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 106 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN B 366 GLN D 312 GLN E 282 GLN E 410 GLN G 389 ASN H 410 GLN I 252 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.086811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.061470 restraints weight = 36191.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.061113 restraints weight = 30879.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.061102 restraints weight = 30010.427| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13557 Z= 0.167 Angle : 0.556 5.972 18390 Z= 0.284 Chirality : 0.043 0.137 2199 Planarity : 0.004 0.046 2352 Dihedral : 4.043 25.042 1836 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.14 % Allowed : 2.51 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1734 helix: 2.50 (0.21), residues: 675 sheet: 0.68 (0.26), residues: 285 loop : -0.88 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 419 HIS 0.008 0.001 HIS I 431 PHE 0.017 0.002 PHE E 408 TYR 0.012 0.002 TYR G 365 ARG 0.010 0.001 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 693) hydrogen bonds : angle 3.58376 ( 2055) covalent geometry : bond 0.00396 (13557) covalent geometry : angle 0.55562 (18390) *********************** 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 188 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 TYR cc_start: 0.7205 (p90) cc_final: 0.5669 (t80) REVERT: B 236 ARG cc_start: 0.7908 (tpp-160) cc_final: 0.6004 (tmt170) REVERT: B 350 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 377 MET cc_start: 0.8363 (mpp) cc_final: 0.8085 (mpp) REVERT: D 229 ASP cc_start: 0.8168 (m-30) cc_final: 0.7926 (m-30) REVERT: E 336 LYS cc_start: 0.7213 (mmmt) cc_final: 0.6874 (mmmt) REVERT: E 397 VAL cc_start: 0.6307 (t) cc_final: 0.6044 (t) REVERT: E 402 GLU cc_start: 0.7124 (tp30) cc_final: 0.6464 (mm-30) REVERT: F 227 TYR cc_start: 0.7292 (p90) cc_final: 0.5950 (t80) REVERT: F 236 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.6202 (ttt180) REVERT: F 242 ARG cc_start: 0.8748 (ttm-80) cc_final: 0.8514 (ttm110) REVERT: F 434 VAL cc_start: 0.9604 (t) cc_final: 0.9362 (m) REVERT: F 444 ARG cc_start: 0.4630 (mtt-85) cc_final: 0.4183 (mtt90) REVERT: H 326 GLN cc_start: 0.9070 (mt0) cc_final: 0.8827 (mm-40) REVERT: I 227 TYR cc_start: 0.6996 (p90) cc_final: 0.6167 (t80) REVERT: I 236 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.6264 (tmt170) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.3993 time to fit residues: 99.0141 Evaluate side-chains 154 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 131 optimal weight: 0.0170 chunk 140 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 286 HIS C 410 GLN D 326 ASN E 282 GLN E 410 GLN H 410 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.086383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.061623 restraints weight = 35943.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.061242 restraints weight = 30689.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.061052 restraints weight = 30368.896| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13557 Z= 0.155 Angle : 0.551 6.927 18390 Z= 0.279 Chirality : 0.043 0.135 2199 Planarity : 0.005 0.059 2352 Dihedral : 4.067 20.283 1836 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.14 % Allowed : 1.63 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1734 helix: 2.42 (0.20), residues: 675 sheet: 0.70 (0.26), residues: 285 loop : -0.84 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 419 HIS 0.005 0.001 HIS I 431 PHE 0.016 0.002 PHE I 253 TYR 0.016 0.002 TYR H 316 ARG 0.013 0.001 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 693) hydrogen bonds : angle 3.52833 ( 2055) covalent geometry : bond 0.00370 (13557) covalent geometry : angle 0.55121 (18390) *********************** 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 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 TYR cc_start: 0.7335 (p90) cc_final: 0.5599 (t80) REVERT: B 235 MET cc_start: 0.6584 (tpt) cc_final: 0.6178 (tpp) REVERT: B 236 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.5938 (tmt170) REVERT: B 350 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7692 (tm-30) REVERT: B 377 MET cc_start: 0.8394 (mpp) cc_final: 0.7987 (mpp) REVERT: D 229 ASP cc_start: 0.8255 (m-30) cc_final: 0.7956 (m-30) REVERT: E 336 LYS cc_start: 0.7312 (mmmt) cc_final: 0.6999 (mmmt) REVERT: E 397 VAL cc_start: 0.6314 (t) cc_final: 0.6089 (t) REVERT: E 402 GLU cc_start: 0.7383 (tp30) cc_final: 0.6729 (mm-30) REVERT: F 227 TYR cc_start: 0.7337 (p90) cc_final: 0.5978 (t80) REVERT: F 236 ARG cc_start: 0.7910 (tpp-160) cc_final: 0.6254 (ttt180) REVERT: F 242 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8479 (ttm110) REVERT: F 434 VAL cc_start: 0.9587 (t) cc_final: 0.9330 (m) REVERT: F 444 ARG cc_start: 0.4623 (mtt-85) cc_final: 0.4207 (mtt90) REVERT: H 298 PHE cc_start: 0.7358 (m-10) cc_final: 0.7135 (m-80) REVERT: I 227 TYR cc_start: 0.7097 (p90) cc_final: 0.6187 (t80) REVERT: I 236 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.6274 (tmt170) REVERT: I 356 ARG cc_start: 0.8724 (ttm-80) cc_final: 0.8336 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.3673 time to fit residues: 95.2156 Evaluate side-chains 164 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN B 382 GLN E 282 GLN H 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.059698 restraints weight = 36555.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.059158 restraints weight = 35553.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.059855 restraints weight = 30599.991| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13557 Z= 0.229 Angle : 0.611 6.578 18390 Z= 0.309 Chirality : 0.044 0.145 2199 Planarity : 0.005 0.064 2352 Dihedral : 4.401 21.607 1836 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.07 % Allowed : 0.88 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1734 helix: 2.21 (0.20), residues: 675 sheet: 0.62 (0.26), residues: 285 loop : -0.89 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 419 HIS 0.003 0.001 HIS I 431 PHE 0.018 0.002 PHE B 253 TYR 0.013 0.002 TYR H 316 ARG 0.013 0.001 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 693) hydrogen bonds : angle 3.78727 ( 2055) covalent geometry : bond 0.00549 (13557) covalent geometry : angle 0.61093 (18390) *********************** 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 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 412 MET cc_start: 0.6807 (ptp) cc_final: 0.6387 (ptp) REVERT: C 422 LYS cc_start: 0.4037 (pptt) cc_final: 0.3304 (pptt) REVERT: B 227 TYR cc_start: 0.7395 (p90) cc_final: 0.5375 (t80) REVERT: B 236 ARG cc_start: 0.7915 (tpp-160) cc_final: 0.6169 (ttt180) REVERT: B 350 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7729 (tm-30) REVERT: B 377 MET cc_start: 0.8440 (mpp) cc_final: 0.7941 (mpp) REVERT: D 229 ASP cc_start: 0.8258 (m-30) cc_final: 0.7945 (m-30) REVERT: E 336 LYS cc_start: 0.7625 (mmmt) cc_final: 0.7283 (mmmt) REVERT: E 402 GLU cc_start: 0.7364 (tp30) cc_final: 0.7024 (mm-30) REVERT: F 227 TYR cc_start: 0.7356 (p90) cc_final: 0.5720 (t80) REVERT: F 236 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.6371 (ttt180) REVERT: F 242 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8557 (ttm110) REVERT: F 434 VAL cc_start: 0.9628 (t) cc_final: 0.9384 (m) REVERT: F 444 ARG cc_start: 0.4711 (mtt-85) cc_final: 0.4193 (mtt180) REVERT: H 402 GLU cc_start: 0.6493 (mm-30) cc_final: 0.5913 (mm-30) REVERT: I 227 TYR cc_start: 0.7068 (p90) cc_final: 0.5951 (t80) REVERT: I 236 ARG cc_start: 0.7935 (tpp-160) cc_final: 0.6281 (tmt170) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.3843 time to fit residues: 101.3309 Evaluate side-chains 173 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 46 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.086943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.062497 restraints weight = 35520.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.061898 restraints weight = 29644.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.061762 restraints weight = 30513.688| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13557 Z= 0.112 Angle : 0.541 7.695 18390 Z= 0.272 Chirality : 0.042 0.137 2199 Planarity : 0.005 0.062 2352 Dihedral : 4.020 20.309 1836 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1734 helix: 2.49 (0.20), residues: 675 sheet: 0.57 (0.27), residues: 321 loop : -0.73 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 419 HIS 0.003 0.001 HIS I 431 PHE 0.018 0.002 PHE C 408 TYR 0.012 0.001 TYR G 365 ARG 0.014 0.001 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 693) hydrogen bonds : angle 3.42927 ( 2055) covalent geometry : bond 0.00265 (13557) covalent geometry : angle 0.54081 (18390) *********************** 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 195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 422 LYS cc_start: 0.3753 (pptt) cc_final: 0.3197 (pptt) REVERT: B 227 TYR cc_start: 0.7564 (p90) cc_final: 0.5489 (t80) REVERT: B 236 ARG cc_start: 0.7686 (tpp-160) cc_final: 0.6058 (ttt180) REVERT: B 350 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7679 (tm-30) REVERT: B 377 MET cc_start: 0.8380 (mpp) cc_final: 0.7881 (mpp) REVERT: D 229 ASP cc_start: 0.8252 (m-30) cc_final: 0.7955 (m-30) REVERT: E 336 LYS cc_start: 0.7540 (mmmt) cc_final: 0.7288 (mmmt) REVERT: E 402 GLU cc_start: 0.7133 (tp30) cc_final: 0.6899 (mm-30) REVERT: F 227 TYR cc_start: 0.7456 (p90) cc_final: 0.5758 (t80) REVERT: F 236 ARG cc_start: 0.7852 (tpp-160) cc_final: 0.6309 (ttt180) REVERT: F 242 ARG cc_start: 0.8712 (ttm-80) cc_final: 0.8490 (ttm110) REVERT: F 434 VAL cc_start: 0.9560 (t) cc_final: 0.9311 (m) REVERT: F 444 ARG cc_start: 0.4549 (mtt-85) cc_final: 0.4128 (mtt90) REVERT: G 375 MET cc_start: 0.8931 (mmm) cc_final: 0.8359 (mmm) REVERT: H 336 LYS cc_start: 0.7361 (tppt) cc_final: 0.6953 (mmmt) REVERT: H 402 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6416 (mm-30) REVERT: I 227 TYR cc_start: 0.7228 (p90) cc_final: 0.6039 (t80) REVERT: I 236 ARG cc_start: 0.7981 (tpp-160) cc_final: 0.6277 (tmt170) REVERT: I 410 ASN cc_start: 0.8499 (m-40) cc_final: 0.8109 (m-40) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3532 time to fit residues: 90.9862 Evaluate side-chains 177 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 16 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 168 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 282 GLN E 410 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.064086 restraints weight = 35704.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.063410 restraints weight = 30610.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.063690 restraints weight = 30220.176| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.6799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13557 Z= 0.098 Angle : 0.539 6.878 18390 Z= 0.272 Chirality : 0.043 0.154 2199 Planarity : 0.005 0.059 2352 Dihedral : 3.865 19.718 1836 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1734 helix: 2.60 (0.20), residues: 675 sheet: 0.57 (0.27), residues: 327 loop : -0.51 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 419 HIS 0.002 0.001 HIS I 431 PHE 0.021 0.001 PHE C 408 TYR 0.012 0.001 TYR C 316 ARG 0.014 0.001 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.02719 ( 693) hydrogen bonds : angle 3.30885 ( 2055) covalent geometry : bond 0.00228 (13557) covalent geometry : angle 0.53931 (18390) ********************** 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 204 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7295 (tm-30) REVERT: C 422 LYS cc_start: 0.3494 (pptt) cc_final: 0.3240 (pptt) REVERT: B 227 TYR cc_start: 0.7452 (p90) cc_final: 0.5416 (t80) REVERT: B 236 ARG cc_start: 0.7743 (tpp-160) cc_final: 0.5996 (tmt170) REVERT: B 350 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 377 MET cc_start: 0.8349 (mpp) cc_final: 0.7924 (mpp) REVERT: D 229 ASP cc_start: 0.8144 (m-30) cc_final: 0.7819 (m-30) REVERT: E 336 LYS cc_start: 0.7521 (mmmt) cc_final: 0.7236 (mmmt) REVERT: E 397 VAL cc_start: 0.6037 (t) cc_final: 0.5674 (t) REVERT: E 402 GLU cc_start: 0.7240 (tp30) cc_final: 0.6803 (mm-30) REVERT: F 227 TYR cc_start: 0.7300 (p90) cc_final: 0.5776 (t80) REVERT: F 236 ARG cc_start: 0.7832 (tpp-160) cc_final: 0.6349 (ttt180) REVERT: F 410 ASN cc_start: 0.8429 (m110) cc_final: 0.8047 (m-40) REVERT: F 434 VAL cc_start: 0.9514 (t) cc_final: 0.9296 (m) REVERT: F 444 ARG cc_start: 0.4572 (mtt-85) cc_final: 0.4124 (mtt90) REVERT: G 375 MET cc_start: 0.8826 (mmm) cc_final: 0.8278 (mmm) REVERT: H 336 LYS cc_start: 0.7174 (tppt) cc_final: 0.6791 (mmmt) REVERT: H 402 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6645 (mm-30) REVERT: I 227 TYR cc_start: 0.7166 (p90) cc_final: 0.5798 (t80) REVERT: I 236 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.6263 (tmt170) REVERT: I 356 ARG cc_start: 0.8709 (ttm-80) cc_final: 0.8422 (mtm-85) REVERT: I 410 ASN cc_start: 0.8496 (m-40) cc_final: 0.8094 (m-40) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3464 time to fit residues: 93.1368 Evaluate side-chains 170 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 23 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN B 269 GLN E 282 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.085497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.061445 restraints weight = 36232.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.060131 restraints weight = 32555.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.060157 restraints weight = 36646.962| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13557 Z= 0.174 Angle : 0.576 7.452 18390 Z= 0.293 Chirality : 0.043 0.141 2199 Planarity : 0.005 0.070 2352 Dihedral : 4.062 19.555 1836 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1734 helix: 2.51 (0.20), residues: 675 sheet: 0.77 (0.26), residues: 285 loop : -0.60 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 419 HIS 0.003 0.001 HIS I 431 PHE 0.022 0.002 PHE H 408 TYR 0.013 0.002 TYR C 316 ARG 0.015 0.001 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 693) hydrogen bonds : angle 3.55864 ( 2055) covalent geometry : bond 0.00420 (13557) covalent geometry : angle 0.57556 (18390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4001.72 seconds wall clock time: 70 minutes 58.10 seconds (4258.10 seconds total)