Starting phenix.real_space_refine on Wed Mar 4 16:34:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lg1_23310/03_2026/7lg1_23310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lg1_23310/03_2026/7lg1_23310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lg1_23310/03_2026/7lg1_23310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lg1_23310/03_2026/7lg1_23310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lg1_23310/03_2026/7lg1_23310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lg1_23310/03_2026/7lg1_23310.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 76 5.16 5 C 9788 2.51 5 N 2428 2.21 5 O 2720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15017 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3729 Chain: "B" Number of atoms: 3730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3729 Chain: "C" Number of atoms: 3730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3729 Chain: "D" Number of atoms: 3730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3729 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N ATHR A 362 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 362 " occ=0.50 residue: pdb=" N AILE A 363 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 363 " occ=0.50 residue: pdb=" N AGLY A 364 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 364 " occ=0.50 residue: pdb=" N AGLN A 365 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 365 " occ=0.50 residue: pdb=" N ATHR A 366 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 366 " occ=0.50 residue: pdb=" N APRO A 367 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO A 367 " occ=0.50 residue: pdb=" N ATHR B 362 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 362 " occ=0.50 residue: pdb=" N AILE B 363 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE B 363 " occ=0.50 residue: pdb=" N AGLY B 364 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 364 " occ=0.50 residue: pdb=" N AGLN B 365 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 365 " occ=0.50 residue: pdb=" N ATHR B 366 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 366 " occ=0.50 residue: pdb=" N APRO B 367 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO B 367 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 5.16, per 1000 atoms: 0.34 Number of scatterers: 15017 At special positions: 0 Unit cell: (95.589, 95.589, 114.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 76 16.00 P 4 15.00 O 2720 8.00 N 2428 7.00 C 9788 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: 1.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3448 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 66.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.523A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.268A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.536A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.587A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.770A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.733A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 424 removed outlier: 3.518A pdb=" N GLY A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 removed outlier: 3.524A pdb=" N VAL A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 removed outlier: 5.039A pdb=" N GLU A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 removed outlier: 4.237A pdb=" N GLU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.523A pdb=" N TYR B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 5.268A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.536A pdb=" N TYR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.770A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.734A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 326 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 371 through 424 removed outlier: 3.518A pdb=" N GLY B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ARG B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 449 through 455 removed outlier: 3.524A pdb=" N VAL B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 removed outlier: 5.039A pdb=" N GLU B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 4.237A pdb=" N GLU B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.523A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.268A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.535A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.770A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.733A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'C' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 removed outlier: 3.524A pdb=" N VAL C 453 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 removed outlier: 5.039A pdb=" N GLU C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 removed outlier: 4.237A pdb=" N GLU C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.523A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.267A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.536A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 removed outlier: 3.587A pdb=" N ILE D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.770A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.733A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 290 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 424 removed outlier: 3.518A pdb=" N GLY D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA D 406 " --> pdb=" O ASN D 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG D 407 " --> pdb=" O MET D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 removed outlier: 3.524A pdb=" N VAL D 453 " --> pdb=" O ASP D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 471 removed outlier: 5.039A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 removed outlier: 4.237A pdb=" N GLU D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 550 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS D 605 " --> pdb=" O GLN D 601 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 500 removed outlier: 7.058A pdb=" N LYS A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 526 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 568 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 524 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 570 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.495A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 526 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 568 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 524 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 570 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 500 removed outlier: 7.059A pdb=" N LYS B 566 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL B 526 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE B 568 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 524 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR B 570 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY B 522 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP B 572 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 505 through 507 removed outlier: 6.495A pdb=" N TYR B 505 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER B 567 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS B 566 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL B 526 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE B 568 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 524 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR B 570 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY B 522 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP B 572 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 500 removed outlier: 7.059A pdb=" N LYS C 566 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL C 526 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 568 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 524 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR C 570 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY C 522 " --> pdb=" O TYR C 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP C 572 " --> pdb=" O LYS C 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.495A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS C 566 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL C 526 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 568 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 524 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR C 570 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY C 522 " --> pdb=" O TYR C 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP C 572 " --> pdb=" O LYS C 520 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 7.058A pdb=" N LYS D 566 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL D 526 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 568 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 524 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR D 570 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY D 522 " --> pdb=" O TYR D 570 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.494A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS D 566 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL D 526 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 568 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 524 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR D 570 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY D 522 " --> pdb=" O TYR D 570 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 1.90 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: 4395 1.34 - 1.45: 2441 1.45 - 1.57: 8400 1.57 - 1.69: 8 1.69 - 1.81: 128 Bond restraints: 15372 Sorted by residual: bond pdb=" O1A PCG C 701 " pdb=" PA PCG C 701 " ideal model delta sigma weight residual 1.582 1.477 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O1A PCG B 701 " pdb=" PA PCG B 701 " ideal model delta sigma weight residual 1.582 1.477 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O1A PCG D 701 " pdb=" PA PCG D 701 " ideal model delta sigma weight residual 1.582 1.477 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O1A PCG A 701 " pdb=" PA PCG A 701 " ideal model delta sigma weight residual 1.582 1.477 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C1' PCG C 701 " pdb=" O4' PCG C 701 " ideal model delta sigma weight residual 1.409 1.477 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 15367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 20356 1.86 - 3.71: 356 3.71 - 5.57: 92 5.57 - 7.42: 32 7.42 - 9.28: 28 Bond angle restraints: 20864 Sorted by residual: angle pdb=" N BILE D 363 " pdb=" CA BILE D 363 " pdb=" C BILE D 363 " ideal model delta sigma weight residual 111.45 104.23 7.22 9.30e-01 1.16e+00 6.03e+01 angle pdb=" N BILE A 363 " pdb=" CA BILE A 363 " pdb=" C BILE A 363 " ideal model delta sigma weight residual 111.45 104.24 7.21 9.30e-01 1.16e+00 6.01e+01 angle pdb=" N BILE C 363 " pdb=" CA BILE C 363 " pdb=" C BILE C 363 " ideal model delta sigma weight residual 111.45 104.26 7.19 9.30e-01 1.16e+00 5.97e+01 angle pdb=" N BILE B 363 " pdb=" CA BILE B 363 " pdb=" C BILE B 363 " ideal model delta sigma weight residual 111.45 104.28 7.17 9.30e-01 1.16e+00 5.95e+01 angle pdb=" N AILE D 363 " pdb=" CA AILE D 363 " pdb=" C AILE D 363 " ideal model delta sigma weight residual 111.58 105.26 6.32 1.06e+00 8.90e-01 3.56e+01 ... (remaining 20859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.98: 8896 28.98 - 57.96: 292 57.96 - 86.94: 8 86.94 - 115.92: 4 115.92 - 144.90: 12 Dihedral angle restraints: 9212 sinusoidal: 3828 harmonic: 5384 Sorted by residual: dihedral pdb=" C3' PCG A 701 " pdb=" O3' PCG A 701 " pdb=" PA PCG A 701 " pdb=" O1A PCG A 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.69 -144.90 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG D 701 " pdb=" O3' PCG D 701 " pdb=" PA PCG D 701 " pdb=" O1A PCG D 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.69 -144.90 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG B 701 " pdb=" O3' PCG B 701 " pdb=" PA PCG B 701 " pdb=" O1A PCG B 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.69 -144.90 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 9209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2292 0.131 - 0.261: 40 0.261 - 0.392: 8 0.392 - 0.522: 0 0.522 - 0.653: 4 Chirality restraints: 2344 Sorted by residual: chirality pdb=" PA PCG D 701 " pdb=" O2A PCG D 701 " pdb=" O3' PCG D 701 " pdb=" O5' PCG D 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.35 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" PA PCG C 701 " pdb=" O2A PCG C 701 " pdb=" O3' PCG C 701 " pdb=" O5' PCG C 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.35 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" PA PCG A 701 " pdb=" O2A PCG A 701 " pdb=" O3' PCG A 701 " pdb=" O5' PCG A 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.35 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 2341 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ATHR A 366 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ATHR A 366 " 0.038 2.00e-02 2.50e+03 pdb=" O ATHR A 366 " -0.014 2.00e-02 2.50e+03 pdb=" N APRO A 367 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ATHR B 366 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ATHR B 366 " -0.038 2.00e-02 2.50e+03 pdb=" O ATHR B 366 " 0.014 2.00e-02 2.50e+03 pdb=" N APRO B 367 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ATHR D 366 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ATHR D 366 " 0.038 2.00e-02 2.50e+03 pdb=" O ATHR D 366 " -0.014 2.00e-02 2.50e+03 pdb=" N APRO D 367 " -0.013 2.00e-02 2.50e+03 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2680 2.76 - 3.30: 15921 3.30 - 3.83: 27376 3.83 - 4.37: 33009 4.37 - 4.90: 54447 Nonbonded interactions: 133433 Sorted by model distance: nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE B 216 " pdb=" OG1 THR B 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE A 216 " pdb=" OG1 THR A 219 " model vdw 2.226 3.040 nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.267 3.040 ... (remaining 133428 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 361 or resid 368 through 701)) selection = (chain 'B' and (resid 156 through 361 or resid 368 through 701)) selection = (chain 'C' and (resid 156 through 361 or resid 368 through 701)) selection = (chain 'D' and (resid 156 through 361 or resid 368 through 701)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.450 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.580 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.005 0.105 15372 Z= 0.251 Angle : 0.754 9.278 20864 Z= 0.445 Chirality : 0.055 0.653 2344 Planarity : 0.005 0.049 2580 Dihedral : 15.026 144.897 5764 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.24 % Allowed : 2.93 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1824 helix: -0.53 (0.14), residues: 1080 sheet: -1.26 (0.82), residues: 56 loop : -1.23 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 561 TYR 0.014 0.001 TYR B 349 PHE 0.015 0.002 PHE C 389 TRP 0.024 0.002 TRP C 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00494 (15372) covalent geometry : angle 0.75351 (20864) hydrogen bonds : bond 0.12267 ( 904) hydrogen bonds : angle 6.69324 ( 2652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 330 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 LYS cc_start: 0.7574 (tppt) cc_final: 0.7369 (tptp) REVERT: A 281 MET cc_start: 0.8286 (ttp) cc_final: 0.8040 (ttm) REVERT: A 286 GLN cc_start: 0.7563 (pp30) cc_final: 0.7113 (tm130) REVERT: A 293 ASN cc_start: 0.7245 (m-40) cc_final: 0.6783 (m-40) REVERT: A 415 ASP cc_start: 0.7232 (m-30) cc_final: 0.7018 (m-30) REVERT: A 431 GLU cc_start: 0.7096 (tt0) cc_final: 0.6841 (mt-10) REVERT: A 432 LYS cc_start: 0.7138 (mttm) cc_final: 0.6627 (ttpt) REVERT: A 459 ASP cc_start: 0.6236 (m-30) cc_final: 0.5867 (t0) REVERT: A 505 TYR cc_start: 0.7652 (m-80) cc_final: 0.7423 (m-80) REVERT: A 520 LYS cc_start: 0.7071 (tttm) cc_final: 0.6724 (ttpt) REVERT: A 521 GLU cc_start: 0.6931 (tt0) cc_final: 0.6128 (tp30) REVERT: A 566 LYS cc_start: 0.7943 (ptmt) cc_final: 0.7723 (ttpt) REVERT: B 239 LYS cc_start: 0.7576 (tppt) cc_final: 0.7372 (tptp) REVERT: B 281 MET cc_start: 0.8290 (ttp) cc_final: 0.8044 (ttm) REVERT: B 286 GLN cc_start: 0.7563 (pp30) cc_final: 0.7120 (tm130) REVERT: B 293 ASN cc_start: 0.7245 (m-40) cc_final: 0.6781 (m-40) REVERT: B 415 ASP cc_start: 0.7230 (m-30) cc_final: 0.7014 (m-30) REVERT: B 431 GLU cc_start: 0.7093 (tt0) cc_final: 0.6841 (mt-10) REVERT: B 432 LYS cc_start: 0.7098 (mttm) cc_final: 0.6579 (ttpt) REVERT: B 459 ASP cc_start: 0.6237 (m-30) cc_final: 0.5866 (t0) REVERT: B 505 TYR cc_start: 0.7674 (m-80) cc_final: 0.7436 (m-80) REVERT: B 520 LYS cc_start: 0.7067 (tttm) cc_final: 0.6716 (ttpt) REVERT: B 521 GLU cc_start: 0.6961 (tt0) cc_final: 0.6151 (tp30) REVERT: B 566 LYS cc_start: 0.7945 (ptmt) cc_final: 0.7728 (ttpt) REVERT: C 226 GLN cc_start: 0.6516 (mm110) cc_final: 0.5999 (mm-40) REVERT: C 281 MET cc_start: 0.8284 (ttp) cc_final: 0.8036 (ttm) REVERT: C 293 ASN cc_start: 0.7226 (m-40) cc_final: 0.6755 (m-40) REVERT: C 415 ASP cc_start: 0.7230 (m-30) cc_final: 0.7022 (m-30) REVERT: C 431 GLU cc_start: 0.7090 (tt0) cc_final: 0.6834 (mt-10) REVERT: C 432 LYS cc_start: 0.7097 (mttm) cc_final: 0.6577 (ttpt) REVERT: C 459 ASP cc_start: 0.6238 (m-30) cc_final: 0.5867 (t0) REVERT: C 505 TYR cc_start: 0.7680 (m-80) cc_final: 0.7413 (m-80) REVERT: C 520 LYS cc_start: 0.7062 (tttm) cc_final: 0.6708 (ttpt) REVERT: C 566 LYS cc_start: 0.7943 (ptmt) cc_final: 0.7728 (ttpt) REVERT: D 226 GLN cc_start: 0.6519 (mm110) cc_final: 0.5998 (mm-40) REVERT: D 281 MET cc_start: 0.8287 (ttp) cc_final: 0.8041 (ttm) REVERT: D 293 ASN cc_start: 0.7226 (m-40) cc_final: 0.6757 (m-40) REVERT: D 415 ASP cc_start: 0.7236 (m-30) cc_final: 0.7027 (m-30) REVERT: D 431 GLU cc_start: 0.7104 (tt0) cc_final: 0.6843 (mt-10) REVERT: D 432 LYS cc_start: 0.7100 (mttm) cc_final: 0.6605 (ttpt) REVERT: D 459 ASP cc_start: 0.6239 (m-30) cc_final: 0.5873 (t0) REVERT: D 505 TYR cc_start: 0.7652 (m-80) cc_final: 0.7430 (m-80) REVERT: D 520 LYS cc_start: 0.7068 (tttm) cc_final: 0.6722 (ttpt) REVERT: D 566 LYS cc_start: 0.7942 (ptmt) cc_final: 0.7722 (ttpt) outliers start: 4 outliers final: 4 residues processed: 334 average time/residue: 0.5977 time to fit residues: 217.9247 Evaluate side-chains 215 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 518 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0050 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN A 468 ASN A 496 GLN A 534 GLN B 402 ASN B 468 ASN B 496 GLN B 534 GLN C 226 GLN C 402 ASN C 468 ASN C 496 GLN C 534 GLN D 226 GLN D 402 ASN D 468 ASN D 496 GLN D 498 GLN D 534 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.188790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.146186 restraints weight = 81922.959| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.88 r_work: 0.2969 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15372 Z= 0.173 Angle : 0.630 8.043 20864 Z= 0.326 Chirality : 0.043 0.171 2344 Planarity : 0.005 0.047 2580 Dihedral : 12.865 152.424 2156 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.85 % Allowed : 12.93 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1824 helix: 0.56 (0.16), residues: 1060 sheet: -0.39 (0.76), residues: 48 loop : -0.57 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 347 TYR 0.018 0.002 TYR B 349 PHE 0.016 0.002 PHE C 389 TRP 0.022 0.002 TRP B 168 HIS 0.003 0.001 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00392 (15372) covalent geometry : angle 0.62978 (20864) hydrogen bonds : bond 0.04496 ( 904) hydrogen bonds : angle 5.22075 ( 2652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.564 Fit side-chains REVERT: A 212 LEU cc_start: 0.8716 (tp) cc_final: 0.8468 (mt) REVERT: A 221 THR cc_start: 0.8235 (t) cc_final: 0.7950 (m) REVERT: A 239 LYS cc_start: 0.7769 (tppt) cc_final: 0.7563 (tppp) REVERT: A 281 MET cc_start: 0.9068 (ttp) cc_final: 0.8844 (ttm) REVERT: A 286 GLN cc_start: 0.8248 (pp30) cc_final: 0.7790 (tm130) REVERT: A 293 ASN cc_start: 0.7468 (m-40) cc_final: 0.7106 (m-40) REVERT: A 415 ASP cc_start: 0.8026 (m-30) cc_final: 0.7819 (m-30) REVERT: A 431 GLU cc_start: 0.7494 (tt0) cc_final: 0.7072 (mt-10) REVERT: A 432 LYS cc_start: 0.7369 (mttm) cc_final: 0.6781 (ttpt) REVERT: A 505 TYR cc_start: 0.8063 (m-80) cc_final: 0.7746 (m-80) REVERT: A 520 LYS cc_start: 0.7294 (tttm) cc_final: 0.7003 (ttmt) REVERT: A 540 ASP cc_start: 0.6147 (OUTLIER) cc_final: 0.5705 (m-30) REVERT: A 566 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7833 (ptmm) REVERT: B 212 LEU cc_start: 0.8712 (tp) cc_final: 0.8459 (mt) REVERT: B 221 THR cc_start: 0.8260 (t) cc_final: 0.7966 (m) REVERT: B 239 LYS cc_start: 0.7794 (tppt) cc_final: 0.7573 (tppp) REVERT: B 281 MET cc_start: 0.9088 (ttp) cc_final: 0.8867 (ttm) REVERT: B 286 GLN cc_start: 0.8250 (pp30) cc_final: 0.7840 (tm130) REVERT: B 293 ASN cc_start: 0.7484 (m-40) cc_final: 0.7126 (m-40) REVERT: B 415 ASP cc_start: 0.8025 (m-30) cc_final: 0.7818 (m-30) REVERT: B 431 GLU cc_start: 0.7490 (tt0) cc_final: 0.7064 (mt-10) REVERT: B 432 LYS cc_start: 0.7372 (mttm) cc_final: 0.6797 (ttpt) REVERT: B 505 TYR cc_start: 0.8065 (m-80) cc_final: 0.7740 (m-80) REVERT: B 520 LYS cc_start: 0.7307 (tttm) cc_final: 0.7033 (ttmt) REVERT: B 566 LYS cc_start: 0.8094 (ptmt) cc_final: 0.7874 (ptmm) REVERT: C 212 LEU cc_start: 0.8710 (tp) cc_final: 0.8454 (mt) REVERT: C 221 THR cc_start: 0.8256 (t) cc_final: 0.7957 (m) REVERT: C 281 MET cc_start: 0.9082 (ttp) cc_final: 0.8862 (ttm) REVERT: C 286 GLN cc_start: 0.8196 (pp30) cc_final: 0.7848 (tm130) REVERT: C 293 ASN cc_start: 0.7476 (m-40) cc_final: 0.7117 (m-40) REVERT: C 415 ASP cc_start: 0.8040 (m-30) cc_final: 0.7830 (m-30) REVERT: C 431 GLU cc_start: 0.7545 (tt0) cc_final: 0.7107 (mt-10) REVERT: C 432 LYS cc_start: 0.7356 (mttm) cc_final: 0.6788 (ttpt) REVERT: C 505 TYR cc_start: 0.8047 (m-80) cc_final: 0.7718 (m-80) REVERT: C 520 LYS cc_start: 0.7289 (tttm) cc_final: 0.7037 (ttmt) REVERT: C 521 GLU cc_start: 0.7681 (tt0) cc_final: 0.7134 (tm-30) REVERT: C 566 LYS cc_start: 0.8067 (ptmt) cc_final: 0.7842 (ptmm) REVERT: D 212 LEU cc_start: 0.8716 (tp) cc_final: 0.8464 (mt) REVERT: D 221 THR cc_start: 0.8264 (t) cc_final: 0.7968 (m) REVERT: D 286 GLN cc_start: 0.8200 (pp30) cc_final: 0.7850 (tm130) REVERT: D 293 ASN cc_start: 0.7464 (m-40) cc_final: 0.7105 (m-40) REVERT: D 415 ASP cc_start: 0.8027 (m-30) cc_final: 0.7808 (m-30) REVERT: D 431 GLU cc_start: 0.7513 (tt0) cc_final: 0.7085 (mt-10) REVERT: D 432 LYS cc_start: 0.7355 (mttm) cc_final: 0.6785 (ttpt) REVERT: D 505 TYR cc_start: 0.8038 (m-80) cc_final: 0.7728 (m-80) REVERT: D 520 LYS cc_start: 0.7297 (tttm) cc_final: 0.7039 (ttmt) REVERT: D 521 GLU cc_start: 0.7664 (tt0) cc_final: 0.7114 (tm-30) REVERT: D 566 LYS cc_start: 0.8048 (ptmt) cc_final: 0.7827 (ptmm) outliers start: 14 outliers final: 0 residues processed: 228 average time/residue: 0.5385 time to fit residues: 135.3529 Evaluate side-chains 192 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 395 ASN B 245 GLN B 395 ASN C 226 GLN C 245 GLN C 395 ASN C 496 GLN C 498 GLN D 226 GLN D 245 GLN D 395 ASN D 498 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.190826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.148970 restraints weight = 82283.285| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.89 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15372 Z= 0.142 Angle : 0.608 8.334 20864 Z= 0.314 Chirality : 0.042 0.186 2344 Planarity : 0.005 0.046 2580 Dihedral : 12.780 151.380 2148 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.40 % Allowed : 14.70 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1824 helix: 0.80 (0.16), residues: 1068 sheet: -0.09 (0.79), residues: 48 loop : -0.48 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.020 0.002 TYR A 205 PHE 0.013 0.001 PHE C 389 TRP 0.020 0.002 TRP A 168 HIS 0.002 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00316 (15372) covalent geometry : angle 0.60794 (20864) hydrogen bonds : bond 0.04120 ( 904) hydrogen bonds : angle 4.99144 ( 2652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.655 Fit side-chains REVERT: A 286 GLN cc_start: 0.8006 (pp30) cc_final: 0.7711 (tm130) REVERT: A 293 ASN cc_start: 0.7193 (m-40) cc_final: 0.6894 (m-40) REVERT: A 395 ASN cc_start: 0.6573 (m-40) cc_final: 0.5996 (t0) REVERT: A 409 GLU cc_start: 0.6895 (tp30) cc_final: 0.6592 (tp30) REVERT: A 432 LYS cc_start: 0.7411 (mttm) cc_final: 0.7021 (ttpt) REVERT: B 286 GLN cc_start: 0.8010 (pp30) cc_final: 0.7714 (tm130) REVERT: B 293 ASN cc_start: 0.7180 (m-40) cc_final: 0.6877 (m-40) REVERT: B 395 ASN cc_start: 0.6631 (m-40) cc_final: 0.5998 (t0) REVERT: B 409 GLU cc_start: 0.6860 (tp30) cc_final: 0.6574 (tp30) REVERT: B 413 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7478 (mtp85) REVERT: B 432 LYS cc_start: 0.7398 (mttm) cc_final: 0.7004 (ttpt) REVERT: C 221 THR cc_start: 0.8177 (t) cc_final: 0.7976 (m) REVERT: C 293 ASN cc_start: 0.7187 (m-40) cc_final: 0.6890 (m-40) REVERT: C 395 ASN cc_start: 0.6575 (m-40) cc_final: 0.5986 (t0) REVERT: C 409 GLU cc_start: 0.6858 (tp30) cc_final: 0.6565 (tp30) REVERT: C 432 LYS cc_start: 0.7356 (mttm) cc_final: 0.6954 (ttpt) REVERT: C 521 GLU cc_start: 0.7350 (tt0) cc_final: 0.6929 (tm-30) REVERT: D 293 ASN cc_start: 0.7202 (m-40) cc_final: 0.6900 (m-40) REVERT: D 395 ASN cc_start: 0.6594 (m-40) cc_final: 0.5992 (t0) REVERT: D 409 GLU cc_start: 0.6844 (tp30) cc_final: 0.6564 (tp30) REVERT: D 413 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7483 (mtp85) REVERT: D 432 LYS cc_start: 0.7412 (mttm) cc_final: 0.7009 (ttpt) REVERT: D 521 GLU cc_start: 0.7349 (tt0) cc_final: 0.6936 (tm-30) outliers start: 23 outliers final: 7 residues processed: 230 average time/residue: 0.5712 time to fit residues: 144.5263 Evaluate side-chains 191 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 413 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 118 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN B 498 GLN D 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.189422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144755 restraints weight = 82533.092| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.06 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15372 Z= 0.167 Angle : 0.592 7.211 20864 Z= 0.309 Chirality : 0.042 0.183 2344 Planarity : 0.005 0.045 2580 Dihedral : 12.840 151.581 2148 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.83 % Allowed : 15.67 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1824 helix: 0.73 (0.15), residues: 1092 sheet: 0.15 (0.73), residues: 48 loop : -0.61 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 347 TYR 0.020 0.002 TYR C 205 PHE 0.016 0.002 PHE C 389 TRP 0.020 0.002 TRP A 168 HIS 0.003 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00381 (15372) covalent geometry : angle 0.59238 (20864) hydrogen bonds : bond 0.04160 ( 904) hydrogen bonds : angle 4.87994 ( 2652) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.540 Fit side-chains REVERT: A 286 GLN cc_start: 0.7999 (pp30) cc_final: 0.7740 (tm130) REVERT: A 293 ASN cc_start: 0.7137 (m-40) cc_final: 0.6826 (m-40) REVERT: A 409 GLU cc_start: 0.6936 (tp30) cc_final: 0.6665 (tp30) REVERT: A 413 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7465 (mtp85) REVERT: A 432 LYS cc_start: 0.7341 (mttm) cc_final: 0.6857 (ttpt) REVERT: B 293 ASN cc_start: 0.7127 (m-40) cc_final: 0.6815 (m-40) REVERT: B 409 GLU cc_start: 0.6862 (tp30) cc_final: 0.6595 (tp30) REVERT: B 413 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7476 (mtp85) REVERT: B 432 LYS cc_start: 0.7336 (mttm) cc_final: 0.6850 (ttpt) REVERT: C 293 ASN cc_start: 0.7142 (m-40) cc_final: 0.6829 (m-40) REVERT: C 409 GLU cc_start: 0.6887 (tp30) cc_final: 0.6593 (tp30) REVERT: C 413 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7456 (mtp85) REVERT: C 432 LYS cc_start: 0.7328 (mttm) cc_final: 0.6838 (ttpt) REVERT: C 521 GLU cc_start: 0.7432 (tt0) cc_final: 0.7019 (tm-30) REVERT: D 293 ASN cc_start: 0.7161 (m-40) cc_final: 0.6847 (m-40) REVERT: D 409 GLU cc_start: 0.6890 (tp30) cc_final: 0.6623 (tp30) REVERT: D 413 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7473 (mtp85) REVERT: D 432 LYS cc_start: 0.7299 (mttm) cc_final: 0.6826 (ttpt) REVERT: D 521 GLU cc_start: 0.7426 (tt0) cc_final: 0.7007 (tm-30) outliers start: 30 outliers final: 10 residues processed: 220 average time/residue: 0.5492 time to fit residues: 133.3434 Evaluate side-chains 182 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 518 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 163 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 148 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 498 GLN B 395 ASN B 498 GLN C 395 ASN C 498 GLN D 395 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.191574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148247 restraints weight = 80794.733| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.88 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15372 Z= 0.132 Angle : 0.566 8.854 20864 Z= 0.293 Chirality : 0.042 0.196 2344 Planarity : 0.005 0.048 2580 Dihedral : 12.755 150.769 2148 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.77 % Allowed : 15.67 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1824 helix: 0.89 (0.16), residues: 1068 sheet: 0.43 (0.75), residues: 48 loop : -0.24 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 347 TYR 0.018 0.002 TYR C 199 PHE 0.012 0.001 PHE C 389 TRP 0.020 0.002 TRP A 168 HIS 0.001 0.001 HIS C 422 Details of bonding type rmsd covalent geometry : bond 0.00302 (15372) covalent geometry : angle 0.56573 (20864) hydrogen bonds : bond 0.04014 ( 904) hydrogen bonds : angle 4.73295 ( 2652) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.492 Fit side-chains REVERT: A 286 GLN cc_start: 0.7994 (pp30) cc_final: 0.7739 (tm130) REVERT: A 293 ASN cc_start: 0.6960 (m-40) cc_final: 0.6688 (m-40) REVERT: A 395 ASN cc_start: 0.6418 (m-40) cc_final: 0.5795 (t0) REVERT: A 409 GLU cc_start: 0.6909 (tp30) cc_final: 0.6639 (tp30) REVERT: A 413 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7438 (mtp85) REVERT: A 432 LYS cc_start: 0.7345 (mttm) cc_final: 0.6888 (ttpt) REVERT: B 293 ASN cc_start: 0.6976 (m-40) cc_final: 0.6681 (m-40) REVERT: B 395 ASN cc_start: 0.6418 (m-40) cc_final: 0.5788 (t0) REVERT: B 409 GLU cc_start: 0.6882 (tp30) cc_final: 0.6623 (tp30) REVERT: B 413 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7436 (mtp85) REVERT: B 432 LYS cc_start: 0.7325 (mttm) cc_final: 0.6870 (ttpt) REVERT: B 596 GLU cc_start: 0.5100 (OUTLIER) cc_final: 0.4273 (mp0) REVERT: C 293 ASN cc_start: 0.6979 (m-40) cc_final: 0.6708 (m-40) REVERT: C 409 GLU cc_start: 0.6898 (tp30) cc_final: 0.6611 (tp30) REVERT: C 413 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7437 (mtp85) REVERT: C 432 LYS cc_start: 0.7308 (mttm) cc_final: 0.6853 (ttpt) REVERT: C 521 GLU cc_start: 0.7403 (tt0) cc_final: 0.7009 (tm-30) REVERT: C 596 GLU cc_start: 0.5082 (OUTLIER) cc_final: 0.4267 (mp0) REVERT: D 293 ASN cc_start: 0.6994 (m-40) cc_final: 0.6721 (m-40) REVERT: D 409 GLU cc_start: 0.6892 (tp30) cc_final: 0.6632 (tp30) REVERT: D 413 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7442 (mtp85) REVERT: D 432 LYS cc_start: 0.7350 (mttm) cc_final: 0.6894 (ttpt) REVERT: D 521 GLU cc_start: 0.7405 (tt0) cc_final: 0.7014 (tm-30) outliers start: 29 outliers final: 8 residues processed: 217 average time/residue: 0.5201 time to fit residues: 125.1777 Evaluate side-chains 190 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 168 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 226 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.189730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145413 restraints weight = 85574.746| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.16 r_work: 0.2965 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15372 Z= 0.170 Angle : 0.603 9.703 20864 Z= 0.315 Chirality : 0.043 0.179 2344 Planarity : 0.005 0.047 2580 Dihedral : 12.812 150.813 2148 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.52 % Allowed : 16.28 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1824 helix: 0.63 (0.15), residues: 1092 sheet: 0.61 (0.72), residues: 48 loop : -0.18 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 347 TYR 0.019 0.002 TYR D 349 PHE 0.015 0.002 PHE A 389 TRP 0.019 0.002 TRP C 168 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00391 (15372) covalent geometry : angle 0.60301 (20864) hydrogen bonds : bond 0.04188 ( 904) hydrogen bonds : angle 4.80648 ( 2652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.574 Fit side-chains REVERT: A 286 GLN cc_start: 0.8351 (pp30) cc_final: 0.7995 (tm130) REVERT: A 293 ASN cc_start: 0.7341 (m-40) cc_final: 0.7007 (m-40) REVERT: A 296 ASN cc_start: 0.8549 (m-40) cc_final: 0.8297 (m-40) REVERT: A 395 ASN cc_start: 0.6880 (m-40) cc_final: 0.6020 (t0) REVERT: A 413 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7616 (mtp85) REVERT: A 432 LYS cc_start: 0.7338 (mttm) cc_final: 0.6680 (ttpt) REVERT: A 521 GLU cc_start: 0.7822 (tt0) cc_final: 0.7173 (tm-30) REVERT: B 293 ASN cc_start: 0.7360 (m-40) cc_final: 0.7020 (m-40) REVERT: B 296 ASN cc_start: 0.8541 (m-40) cc_final: 0.8288 (m-40) REVERT: B 395 ASN cc_start: 0.6842 (m-40) cc_final: 0.5978 (t0) REVERT: B 413 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7616 (mtp85) REVERT: B 432 LYS cc_start: 0.7381 (mttm) cc_final: 0.6766 (ttpt) REVERT: B 596 GLU cc_start: 0.5492 (OUTLIER) cc_final: 0.4240 (mp0) REVERT: C 262 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6705 (tttp) REVERT: C 293 ASN cc_start: 0.7360 (m-40) cc_final: 0.7020 (m-40) REVERT: C 413 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7655 (mtp85) REVERT: C 432 LYS cc_start: 0.7349 (mttm) cc_final: 0.6742 (ttpt) REVERT: C 498 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: C 521 GLU cc_start: 0.7881 (tt0) cc_final: 0.7248 (tm-30) REVERT: C 596 GLU cc_start: 0.5415 (OUTLIER) cc_final: 0.4198 (mp0) REVERT: D 293 ASN cc_start: 0.7368 (m-40) cc_final: 0.7027 (m-40) REVERT: D 413 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7615 (mtp85) REVERT: D 432 LYS cc_start: 0.7334 (mttm) cc_final: 0.6673 (ttpt) REVERT: D 521 GLU cc_start: 0.7883 (tt0) cc_final: 0.7254 (tm-30) outliers start: 25 outliers final: 6 residues processed: 186 average time/residue: 0.5619 time to fit residues: 115.8218 Evaluate side-chains 173 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 429 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN D 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.191815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.148964 restraints weight = 84062.529| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.87 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15372 Z= 0.130 Angle : 0.569 11.048 20864 Z= 0.295 Chirality : 0.042 0.172 2344 Planarity : 0.005 0.048 2580 Dihedral : 12.719 150.068 2148 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.71 % Allowed : 15.98 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1824 helix: 0.81 (0.15), residues: 1092 sheet: 0.89 (0.73), residues: 48 loop : -0.04 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.018 0.002 TYR A 199 PHE 0.015 0.001 PHE C 574 TRP 0.020 0.002 TRP D 168 HIS 0.001 0.000 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00295 (15372) covalent geometry : angle 0.56934 (20864) hydrogen bonds : bond 0.03943 ( 904) hydrogen bonds : angle 4.68061 ( 2652) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.586 Fit side-chains REVERT: A 286 GLN cc_start: 0.8022 (pp30) cc_final: 0.7763 (tm130) REVERT: A 293 ASN cc_start: 0.6854 (m-40) cc_final: 0.6625 (m-40) REVERT: A 296 ASN cc_start: 0.8203 (m-40) cc_final: 0.7935 (m-40) REVERT: A 395 ASN cc_start: 0.6132 (m-40) cc_final: 0.5684 (t0) REVERT: A 403 MET cc_start: 0.5741 (ttt) cc_final: 0.5408 (ttm) REVERT: A 409 GLU cc_start: 0.6865 (tp30) cc_final: 0.6563 (tp30) REVERT: A 413 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7557 (mtp85) REVERT: A 430 MET cc_start: 0.6952 (tpp) cc_final: 0.6462 (mtp) REVERT: A 432 LYS cc_start: 0.7330 (mttm) cc_final: 0.6844 (ttpt) REVERT: A 521 GLU cc_start: 0.7481 (tt0) cc_final: 0.7067 (tm-30) REVERT: B 293 ASN cc_start: 0.6846 (m-40) cc_final: 0.6608 (m-40) REVERT: B 296 ASN cc_start: 0.8195 (m-40) cc_final: 0.7926 (m-40) REVERT: B 395 ASN cc_start: 0.6148 (m-40) cc_final: 0.5687 (t0) REVERT: B 403 MET cc_start: 0.5743 (ttt) cc_final: 0.5408 (ttm) REVERT: B 409 GLU cc_start: 0.6848 (tp30) cc_final: 0.6553 (tp30) REVERT: B 413 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7544 (mtp85) REVERT: B 432 LYS cc_start: 0.7330 (mttm) cc_final: 0.6864 (ttpt) REVERT: B 521 GLU cc_start: 0.7425 (tt0) cc_final: 0.7038 (tm-30) REVERT: B 596 GLU cc_start: 0.5112 (OUTLIER) cc_final: 0.4333 (mp0) REVERT: C 293 ASN cc_start: 0.6855 (m-40) cc_final: 0.6613 (m-40) REVERT: C 296 ASN cc_start: 0.8228 (m-40) cc_final: 0.7993 (m-40) REVERT: C 403 MET cc_start: 0.5785 (ttt) cc_final: 0.5420 (ttm) REVERT: C 409 GLU cc_start: 0.6855 (tp30) cc_final: 0.6575 (tp30) REVERT: C 413 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7556 (mtp85) REVERT: C 432 LYS cc_start: 0.7323 (mttm) cc_final: 0.6863 (ttpt) REVERT: C 521 GLU cc_start: 0.7420 (tt0) cc_final: 0.7012 (tm-30) REVERT: C 596 GLU cc_start: 0.5102 (OUTLIER) cc_final: 0.4329 (mp0) REVERT: D 293 ASN cc_start: 0.6850 (m-40) cc_final: 0.6610 (m-40) REVERT: D 296 ASN cc_start: 0.8237 (m-40) cc_final: 0.7986 (m-40) REVERT: D 403 MET cc_start: 0.5699 (ttt) cc_final: 0.5332 (ttm) REVERT: D 409 GLU cc_start: 0.6880 (tp30) cc_final: 0.6587 (tp30) REVERT: D 413 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7437 (mtp85) REVERT: D 430 MET cc_start: 0.6989 (tpp) cc_final: 0.6573 (mtp) REVERT: D 432 LYS cc_start: 0.7348 (mttm) cc_final: 0.6861 (ttpt) REVERT: D 521 GLU cc_start: 0.7402 (tt0) cc_final: 0.6983 (tm-30) outliers start: 28 outliers final: 6 residues processed: 193 average time/residue: 0.5911 time to fit residues: 125.4077 Evaluate side-chains 182 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 413 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 125 optimal weight: 0.0670 chunk 82 optimal weight: 0.3980 chunk 126 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.191888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150375 restraints weight = 85637.027| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.90 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15372 Z= 0.125 Angle : 0.566 11.415 20864 Z= 0.293 Chirality : 0.042 0.171 2344 Planarity : 0.005 0.049 2580 Dihedral : 12.693 149.942 2148 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.71 % Allowed : 16.16 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1824 helix: 0.89 (0.16), residues: 1092 sheet: 1.11 (0.76), residues: 48 loop : 0.05 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 347 TYR 0.017 0.002 TYR B 199 PHE 0.011 0.001 PHE D 389 TRP 0.024 0.002 TRP D 442 HIS 0.001 0.000 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00283 (15372) covalent geometry : angle 0.56646 (20864) hydrogen bonds : bond 0.03878 ( 904) hydrogen bonds : angle 4.64373 ( 2652) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.555 Fit side-chains REVERT: A 286 GLN cc_start: 0.7996 (pp30) cc_final: 0.7755 (tm130) REVERT: A 293 ASN cc_start: 0.6730 (m-40) cc_final: 0.6480 (m110) REVERT: A 296 ASN cc_start: 0.8171 (m-40) cc_final: 0.7887 (m-40) REVERT: A 395 ASN cc_start: 0.6039 (m-40) cc_final: 0.5650 (t0) REVERT: A 403 MET cc_start: 0.5697 (ttt) cc_final: 0.5320 (ttm) REVERT: A 409 GLU cc_start: 0.6824 (tp30) cc_final: 0.6513 (tp30) REVERT: A 413 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7539 (mtp85) REVERT: A 430 MET cc_start: 0.6968 (tpp) cc_final: 0.6448 (mtp) REVERT: A 432 LYS cc_start: 0.7235 (mttm) cc_final: 0.6763 (ttpt) REVERT: A 521 GLU cc_start: 0.7466 (tt0) cc_final: 0.7079 (tm-30) REVERT: B 293 ASN cc_start: 0.6718 (m-40) cc_final: 0.6461 (m110) REVERT: B 296 ASN cc_start: 0.8179 (m-40) cc_final: 0.7902 (m-40) REVERT: B 395 ASN cc_start: 0.6037 (m-40) cc_final: 0.5651 (t0) REVERT: B 403 MET cc_start: 0.5739 (ttt) cc_final: 0.5366 (ttm) REVERT: B 409 GLU cc_start: 0.6814 (tp30) cc_final: 0.6504 (tp30) REVERT: B 413 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7538 (mtp85) REVERT: B 430 MET cc_start: 0.6903 (tpp) cc_final: 0.6659 (ttm) REVERT: B 432 LYS cc_start: 0.7190 (mttm) cc_final: 0.6735 (ttpt) REVERT: B 521 GLU cc_start: 0.7422 (tt0) cc_final: 0.7010 (tm-30) REVERT: B 596 GLU cc_start: 0.5091 (OUTLIER) cc_final: 0.4269 (mp0) REVERT: C 262 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6825 (tttp) REVERT: C 281 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8412 (ttm) REVERT: C 293 ASN cc_start: 0.6764 (m-40) cc_final: 0.6525 (m-40) REVERT: C 296 ASN cc_start: 0.8222 (m-40) cc_final: 0.7969 (m-40) REVERT: C 403 MET cc_start: 0.5739 (ttt) cc_final: 0.5338 (ttm) REVERT: C 413 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7415 (mtp85) REVERT: C 430 MET cc_start: 0.6952 (tpp) cc_final: 0.6705 (ttm) REVERT: C 432 LYS cc_start: 0.7207 (mttm) cc_final: 0.6764 (ttpt) REVERT: C 521 GLU cc_start: 0.7313 (tt0) cc_final: 0.6935 (tm-30) REVERT: C 596 GLU cc_start: 0.5125 (OUTLIER) cc_final: 0.4306 (mp0) REVERT: D 281 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8413 (ttm) REVERT: D 293 ASN cc_start: 0.6773 (m-40) cc_final: 0.6536 (m-40) REVERT: D 296 ASN cc_start: 0.8224 (m-40) cc_final: 0.7975 (m-40) REVERT: D 403 MET cc_start: 0.5743 (ttt) cc_final: 0.5346 (ttm) REVERT: D 413 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7424 (mtp85) REVERT: D 430 MET cc_start: 0.6916 (tpp) cc_final: 0.6516 (mtp) REVERT: D 432 LYS cc_start: 0.7219 (mttm) cc_final: 0.6766 (ttpt) REVERT: D 521 GLU cc_start: 0.7394 (tt0) cc_final: 0.6988 (tm-30) outliers start: 28 outliers final: 5 residues processed: 202 average time/residue: 0.5305 time to fit residues: 118.5500 Evaluate side-chains 192 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 413 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 60 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN C 498 GLN ** C 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.192564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151378 restraints weight = 92883.047| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.01 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15372 Z= 0.149 Angle : 0.593 11.782 20864 Z= 0.305 Chirality : 0.042 0.176 2344 Planarity : 0.005 0.049 2580 Dihedral : 12.711 149.969 2148 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.40 % Allowed : 16.95 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1824 helix: 0.84 (0.15), residues: 1092 sheet: 0.98 (0.74), residues: 48 loop : 0.12 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 407 TYR 0.017 0.002 TYR B 349 PHE 0.013 0.002 PHE D 389 TRP 0.028 0.002 TRP D 442 HIS 0.002 0.001 HIS C 422 Details of bonding type rmsd covalent geometry : bond 0.00342 (15372) covalent geometry : angle 0.59272 (20864) hydrogen bonds : bond 0.03955 ( 904) hydrogen bonds : angle 4.66342 ( 2652) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.564 Fit side-chains REVERT: A 286 GLN cc_start: 0.8043 (pp30) cc_final: 0.7789 (tm130) REVERT: A 293 ASN cc_start: 0.6793 (m-40) cc_final: 0.6546 (m110) REVERT: A 296 ASN cc_start: 0.8165 (m-40) cc_final: 0.7896 (m-40) REVERT: A 395 ASN cc_start: 0.6178 (m-40) cc_final: 0.5781 (t0) REVERT: A 403 MET cc_start: 0.5787 (ttt) cc_final: 0.5361 (ttm) REVERT: A 413 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7545 (mtp85) REVERT: A 430 MET cc_start: 0.6957 (tpp) cc_final: 0.6304 (mtp) REVERT: A 432 LYS cc_start: 0.7237 (mttm) cc_final: 0.6964 (mtmt) REVERT: A 521 GLU cc_start: 0.7478 (tt0) cc_final: 0.7093 (tm-30) REVERT: B 293 ASN cc_start: 0.6804 (m-40) cc_final: 0.6549 (m110) REVERT: B 296 ASN cc_start: 0.8173 (m-40) cc_final: 0.7904 (m-40) REVERT: B 395 ASN cc_start: 0.6124 (m-40) cc_final: 0.5738 (t0) REVERT: B 403 MET cc_start: 0.5762 (ttt) cc_final: 0.5335 (ttm) REVERT: B 413 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7541 (mtp85) REVERT: B 430 MET cc_start: 0.6970 (tpp) cc_final: 0.6766 (ttm) REVERT: B 432 LYS cc_start: 0.7214 (mttm) cc_final: 0.6958 (mtmt) REVERT: B 521 GLU cc_start: 0.7439 (tt0) cc_final: 0.7033 (tm-30) REVERT: B 596 GLU cc_start: 0.5134 (OUTLIER) cc_final: 0.4353 (mp0) REVERT: C 262 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6884 (tttp) REVERT: C 293 ASN cc_start: 0.6819 (m-40) cc_final: 0.6581 (m-40) REVERT: C 296 ASN cc_start: 0.8202 (m-40) cc_final: 0.7936 (m-40) REVERT: C 395 ASN cc_start: 0.6150 (m-40) cc_final: 0.5626 (t0) REVERT: C 403 MET cc_start: 0.5774 (ttt) cc_final: 0.5339 (ttm) REVERT: C 413 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7547 (mtp85) REVERT: C 415 ASP cc_start: 0.7800 (m-30) cc_final: 0.7507 (m-30) REVERT: C 432 LYS cc_start: 0.7219 (mttm) cc_final: 0.6956 (mtmt) REVERT: C 521 GLU cc_start: 0.7277 (tt0) cc_final: 0.6929 (tm-30) REVERT: C 596 GLU cc_start: 0.5127 (OUTLIER) cc_final: 0.4339 (mp0) REVERT: D 281 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8471 (ttm) REVERT: D 293 ASN cc_start: 0.6834 (m-40) cc_final: 0.6579 (m110) REVERT: D 296 ASN cc_start: 0.8207 (m-40) cc_final: 0.7949 (m-40) REVERT: D 395 ASN cc_start: 0.6161 (m-40) cc_final: 0.5638 (t0) REVERT: D 403 MET cc_start: 0.5764 (ttt) cc_final: 0.5339 (ttm) REVERT: D 413 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7464 (mtp85) REVERT: D 430 MET cc_start: 0.6938 (tpp) cc_final: 0.6383 (mtp) REVERT: D 432 LYS cc_start: 0.7236 (mttm) cc_final: 0.6788 (ttpt) REVERT: D 521 GLU cc_start: 0.7377 (tt0) cc_final: 0.6990 (tm-30) outliers start: 23 outliers final: 7 residues processed: 195 average time/residue: 0.5536 time to fit residues: 119.1144 Evaluate side-chains 192 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 413 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 chunk 110 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 86 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN D 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.192234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.150517 restraints weight = 83808.097| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.99 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15372 Z= 0.123 Angle : 0.571 12.482 20864 Z= 0.295 Chirality : 0.042 0.171 2344 Planarity : 0.005 0.049 2580 Dihedral : 12.659 149.435 2148 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.10 % Allowed : 17.44 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.20), residues: 1824 helix: 0.95 (0.16), residues: 1092 sheet: 1.17 (0.77), residues: 48 loop : 0.20 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 407 TYR 0.017 0.001 TYR D 205 PHE 0.012 0.001 PHE B 574 TRP 0.032 0.002 TRP D 442 HIS 0.001 0.001 HIS C 422 Details of bonding type rmsd covalent geometry : bond 0.00278 (15372) covalent geometry : angle 0.57096 (20864) hydrogen bonds : bond 0.03845 ( 904) hydrogen bonds : angle 4.59294 ( 2652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.536 Fit side-chains REVERT: A 286 GLN cc_start: 0.8007 (pp30) cc_final: 0.7771 (tm130) REVERT: A 293 ASN cc_start: 0.6709 (m-40) cc_final: 0.6478 (m110) REVERT: A 296 ASN cc_start: 0.8169 (m-40) cc_final: 0.7883 (m-40) REVERT: A 403 MET cc_start: 0.5673 (ttt) cc_final: 0.5271 (ttm) REVERT: A 409 GLU cc_start: 0.6902 (tp30) cc_final: 0.6572 (tp30) REVERT: A 413 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7550 (mtp85) REVERT: A 430 MET cc_start: 0.6916 (tpp) cc_final: 0.6626 (ttm) REVERT: A 432 LYS cc_start: 0.7189 (mttm) cc_final: 0.6948 (mtmt) REVERT: A 521 GLU cc_start: 0.7461 (tt0) cc_final: 0.7078 (tm-30) REVERT: B 293 ASN cc_start: 0.6733 (m-40) cc_final: 0.6486 (m110) REVERT: B 296 ASN cc_start: 0.8174 (m-40) cc_final: 0.7908 (m-40) REVERT: B 403 MET cc_start: 0.5652 (ttt) cc_final: 0.5248 (ttm) REVERT: B 413 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7514 (mtp85) REVERT: B 430 MET cc_start: 0.6857 (tpp) cc_final: 0.6536 (ttm) REVERT: B 432 LYS cc_start: 0.7216 (mttm) cc_final: 0.6964 (mtmt) REVERT: B 521 GLU cc_start: 0.7428 (tt0) cc_final: 0.7051 (tm-30) REVERT: B 596 GLU cc_start: 0.5079 (OUTLIER) cc_final: 0.4232 (mp0) REVERT: C 262 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6838 (tttp) REVERT: C 281 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8417 (ttm) REVERT: C 293 ASN cc_start: 0.6730 (m-40) cc_final: 0.6487 (m110) REVERT: C 296 ASN cc_start: 0.8180 (m-40) cc_final: 0.7924 (m-40) REVERT: C 403 MET cc_start: 0.5632 (ttt) cc_final: 0.5246 (ttm) REVERT: C 409 GLU cc_start: 0.6909 (tp30) cc_final: 0.6597 (tp30) REVERT: C 413 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7579 (mtp85) REVERT: C 415 ASP cc_start: 0.7779 (m-30) cc_final: 0.7555 (m-30) REVERT: C 432 LYS cc_start: 0.7201 (mttm) cc_final: 0.6948 (mtmt) REVERT: C 521 GLU cc_start: 0.7285 (tt0) cc_final: 0.6911 (tm-30) REVERT: C 596 GLU cc_start: 0.5077 (OUTLIER) cc_final: 0.4228 (mp0) REVERT: D 281 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8425 (ttm) REVERT: D 293 ASN cc_start: 0.6751 (m-40) cc_final: 0.6507 (m110) REVERT: D 296 ASN cc_start: 0.8176 (m-40) cc_final: 0.7909 (m-40) REVERT: D 403 MET cc_start: 0.5650 (ttt) cc_final: 0.5249 (ttm) REVERT: D 413 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7449 (mtp85) REVERT: D 430 MET cc_start: 0.6862 (tpp) cc_final: 0.6633 (ttm) REVERT: D 432 LYS cc_start: 0.7210 (mttm) cc_final: 0.6974 (mtmt) REVERT: D 521 GLU cc_start: 0.7291 (tt0) cc_final: 0.6949 (tm-30) outliers start: 18 outliers final: 6 residues processed: 187 average time/residue: 0.5501 time to fit residues: 114.1442 Evaluate side-chains 194 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 413 ARG Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.192736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.152080 restraints weight = 81585.442| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.89 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15372 Z= 0.147 Angle : 0.598 12.098 20864 Z= 0.307 Chirality : 0.042 0.174 2344 Planarity : 0.005 0.048 2580 Dihedral : 12.694 149.720 2148 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.22 % Allowed : 17.56 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1824 helix: 0.85 (0.15), residues: 1092 sheet: 0.95 (0.74), residues: 48 loop : 0.26 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 407 TYR 0.017 0.002 TYR C 349 PHE 0.013 0.002 PHE C 389 TRP 0.033 0.002 TRP D 442 HIS 0.002 0.001 HIS D 470 Details of bonding type rmsd covalent geometry : bond 0.00337 (15372) covalent geometry : angle 0.59803 (20864) hydrogen bonds : bond 0.03981 ( 904) hydrogen bonds : angle 4.64919 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3872.18 seconds wall clock time: 67 minutes 9.83 seconds (4029.83 seconds total)