Starting phenix.real_space_refine on Sat Mar 7 09:26:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rff_24440/03_2026/7rff_24440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rff_24440/03_2026/7rff_24440.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/7rff_24440/03_2026/7rff_24440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rff_24440/03_2026/7rff_24440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rff_24440/03_2026/7rff_24440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rff_24440/03_2026/7rff_24440.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= 0.240 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 C 12896 2.51 5 N 3504 2.21 5 O 3864 1.98 5 H 20600 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 173 residue(s): 0.03s 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: 41000 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "B" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "C" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "D" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "E" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "F" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "G" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Chain: "H" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5125 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 4 Time building chain proxies: 7.40, per 1000 atoms: 0.18 Number of scatterers: 41000 At special positions: 0 Unit cell: (126, 124.95, 101.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 O 3864 8.00 N 3504 7.00 C 12896 6.00 H 20600 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.2 seconds 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4880 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 24 sheets defined 49.1% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid -18 through -9 Processing helix chain 'A' and resid -8 through -6 No H-bonds generated for 'chain 'A' and resid -8 through -6' Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.525A pdb=" N PHE A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.670A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.929A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid -18 through -8 removed outlier: 3.534A pdb=" N LEU B -8 " --> pdb=" O SER B -12 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.654A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 342 through 356 removed outlier: 3.880A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid -18 through -9 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.583A pdb=" N PHE C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.753A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 342 through 356 removed outlier: 3.926A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid -18 through -9 Processing helix chain 'D' and resid -8 through -6 No H-bonds generated for 'chain 'D' and resid -8 through -6' Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 19 through 25 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 255 through 266 removed outlier: 3.690A pdb=" N ASP D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 342 through 356 removed outlier: 3.909A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid -18 through -9 Processing helix chain 'E' and resid -8 through -6 No H-bonds generated for 'chain 'E' and resid -8 through -6' Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 19 through 25 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 110 removed outlier: 3.551A pdb=" N PHE E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.512A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 342 through 356 removed outlier: 3.911A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid -18 through -9 Processing helix chain 'F' and resid -8 through -6 No H-bonds generated for 'chain 'F' and resid -8 through -6' Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 96 through 110 removed outlier: 3.559A pdb=" N PHE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.714A pdb=" N ASP F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 342 through 356 removed outlier: 3.904A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid -18 through -9 Processing helix chain 'G' and resid -8 through -6 No H-bonds generated for 'chain 'G' and resid -8 through -6' Processing helix chain 'G' and resid 2 through 8 Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 110 Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.737A pdb=" N ASP G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 342 through 356 removed outlier: 3.864A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid -18 through -9 Processing helix chain 'H' and resid -8 through -6 No H-bonds generated for 'chain 'H' and resid -8 through -6' Processing helix chain 'H' and resid 2 through 8 Processing helix chain 'H' and resid 19 through 25 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 110 removed outlier: 3.530A pdb=" N PHE H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.672A pdb=" N ASP H 261 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 Processing helix chain 'H' and resid 342 through 356 removed outlier: 3.871A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 37 removed outlier: 7.989A pdb=" N GLY B 29 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS A 492 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.599A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 37 removed outlier: 7.992A pdb=" N GLY C 29 " --> pdb=" O PHE B 490 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 492 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.600A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 322 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 35 through 37 removed outlier: 7.987A pdb=" N GLY D 29 " --> pdb=" O PHE C 490 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS C 492 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.609A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 322 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.613A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 322 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 28 through 29 Processing sheet with id=AB5, first strand: chain 'E' and resid 35 through 37 removed outlier: 7.969A pdb=" N GLY F 29 " --> pdb=" O PHE E 490 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS E 492 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.592A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG E 322 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 35 through 37 removed outlier: 7.961A pdb=" N GLY G 29 " --> pdb=" O PHE F 490 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS F 492 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.507A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG F 322 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 35 through 37 removed outlier: 7.957A pdb=" N GLY H 29 " --> pdb=" O PHE G 490 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS G 492 " --> pdb=" O GLY H 29 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.607A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG G 322 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.588A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG H 322 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) 962 hydrogen bonds defined for protein. 2745 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: 10.66 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 20568 1.12 - 1.30: 3642 1.30 - 1.48: 7708 1.48 - 1.65: 9146 1.65 - 1.83: 240 Bond restraints: 41304 Sorted by residual: bond pdb=" N HIS F 296 " pdb=" H HIS F 296 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N GLY G 251 " pdb=" H GLY G 251 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLU B 15 " pdb=" H GLU B 15 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 TYR B 348 " pdb=" HD2 TYR B 348 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH2 ARG C 474 " pdb="HH21 ARG C 474 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 41299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 62793 2.61 - 5.22: 9072 5.22 - 7.83: 2626 7.83 - 10.44: 134 10.44 - 13.05: 23 Bond angle restraints: 74648 Sorted by residual: angle pdb=" CA GLY H 324 " pdb=" C GLY H 324 " pdb=" N MET H 325 " ideal model delta sigma weight residual 115.34 120.84 -5.50 8.10e-01 1.52e+00 4.61e+01 angle pdb=" OE1 GLN B 277 " pdb=" CD GLN B 277 " pdb=" NE2 GLN B 277 " ideal model delta sigma weight residual 122.60 116.29 6.31 1.00e+00 1.00e+00 3.98e+01 angle pdb=" CA ASP D 28 " pdb=" CB ASP D 28 " pdb=" CG ASP D 28 " ideal model delta sigma weight residual 112.60 118.67 -6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CA GLY C 324 " pdb=" C GLY C 324 " pdb=" N MET C 325 " ideal model delta sigma weight residual 115.74 120.04 -4.30 7.30e-01 1.88e+00 3.47e+01 angle pdb=" CA GLY B 324 " pdb=" C GLY B 324 " pdb=" N MET B 325 " ideal model delta sigma weight residual 115.34 120.11 -4.77 8.10e-01 1.52e+00 3.46e+01 ... (remaining 74643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 17383 17.98 - 35.96: 1145 35.96 - 53.94: 430 53.94 - 71.92: 359 71.92 - 89.90: 43 Dihedral angle restraints: 19360 sinusoidal: 10656 harmonic: 8704 Sorted by residual: dihedral pdb=" CA GLU F 335 " pdb=" C GLU F 335 " pdb=" N VAL F 336 " pdb=" CA VAL F 336 " ideal model delta harmonic sigma weight residual 180.00 150.17 29.83 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" C VAL B 457 " pdb=" N VAL B 457 " pdb=" CA VAL B 457 " pdb=" CB VAL B 457 " ideal model delta harmonic sigma weight residual -122.00 -136.69 14.69 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" C VAL G 457 " pdb=" N VAL G 457 " pdb=" CA VAL G 457 " pdb=" CB VAL G 457 " ideal model delta harmonic sigma weight residual -122.00 -136.39 14.39 0 2.50e+00 1.60e-01 3.31e+01 ... (remaining 19357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2322 0.094 - 0.188: 772 0.188 - 0.282: 121 0.282 - 0.376: 20 0.376 - 0.470: 5 Chirality restraints: 3240 Sorted by residual: chirality pdb=" CA VAL G 457 " pdb=" N VAL G 457 " pdb=" C VAL G 457 " pdb=" CB VAL G 457 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" CA VAL B 457 " pdb=" N VAL B 457 " pdb=" C VAL B 457 " pdb=" CB VAL B 457 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA VAL E 457 " pdb=" N VAL E 457 " pdb=" C VAL E 457 " pdb=" CB VAL E 457 " both_signs ideal model delta sigma weight residual False 2.44 1.99 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 3237 not shown) Planarity restraints: 6176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 259 " -0.015 9.50e-02 1.11e+02 7.36e-02 1.21e+02 pdb=" NE ARG E 259 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 259 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG E 259 " -0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG E 259 " -0.037 2.00e-02 2.50e+03 pdb="HH11 ARG E 259 " 0.144 2.00e-02 2.50e+03 pdb="HH12 ARG E 259 " -0.042 2.00e-02 2.50e+03 pdb="HH21 ARG E 259 " 0.120 2.00e-02 2.50e+03 pdb="HH22 ARG E 259 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 259 " 0.026 9.50e-02 1.11e+02 7.01e-02 1.09e+02 pdb=" NE ARG F 259 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG F 259 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG F 259 " 0.053 2.00e-02 2.50e+03 pdb=" NH2 ARG F 259 " 0.035 2.00e-02 2.50e+03 pdb="HH11 ARG F 259 " -0.138 2.00e-02 2.50e+03 pdb="HH12 ARG F 259 " 0.039 2.00e-02 2.50e+03 pdb="HH21 ARG F 259 " -0.113 2.00e-02 2.50e+03 pdb="HH22 ARG F 259 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 259 " 0.031 9.50e-02 1.11e+02 6.89e-02 1.04e+02 pdb=" NE ARG B 259 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG B 259 " -0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG B 259 " -0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG B 259 " -0.044 2.00e-02 2.50e+03 pdb="HH11 ARG B 259 " 0.127 2.00e-02 2.50e+03 pdb="HH12 ARG B 259 " -0.032 2.00e-02 2.50e+03 pdb="HH21 ARG B 259 " 0.118 2.00e-02 2.50e+03 pdb="HH22 ARG B 259 " -0.015 2.00e-02 2.50e+03 ... (remaining 6173 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2967 2.20 - 2.80: 76957 2.80 - 3.40: 119226 3.40 - 4.00: 164099 4.00 - 4.60: 239861 Nonbonded interactions: 603110 Sorted by model distance: nonbonded pdb=" HG SER G 26 " pdb=" OD1 ASP G 28 " model vdw 1.602 2.450 nonbonded pdb=" HG SER H 26 " pdb=" OD1 ASP H 28 " model vdw 1.604 2.450 nonbonded pdb=" HG SER C 26 " pdb=" OD1 ASP C 28 " model vdw 1.604 2.450 nonbonded pdb=" HB2 LEU H 321 " pdb="HD11 ILE H 361 " model vdw 1.605 2.440 nonbonded pdb=" HG SER D 26 " pdb=" OD1 ASP D 28 " model vdw 1.607 2.450 ... (remaining 603105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.260 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 39.280 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.012 0.073 20704 Z= 0.721 Angle : 1.833 7.915 27952 Z= 1.233 Chirality : 0.093 0.470 3240 Planarity : 0.013 0.125 3592 Dihedral : 14.113 89.895 7536 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.80 % Favored : 95.90 % Rotamer: Outliers : 1.97 % Allowed : 6.37 % Favored : 91.67 % Cbeta Deviations : 0.20 % 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: -1.34 (0.14), residues: 2632 helix: -0.89 (0.12), residues: 1208 sheet: -0.31 (0.27), residues: 216 loop : -0.85 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 355 TYR 0.098 0.018 TYR B 353 PHE 0.061 0.011 PHE E 44 HIS 0.011 0.003 HIS G 288 Details of bonding type rmsd covalent geometry : bond 0.01188 (20704) covalent geometry : angle 1.83323 (27952) hydrogen bonds : bond 0.18601 ( 962) hydrogen bonds : angle 7.87418 ( 2745) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 635 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6634 (pp20) cc_final: 0.6400 (pp20) REVERT: A 21 GLN cc_start: 0.8289 (tt0) cc_final: 0.7913 (tt0) REVERT: A 60 THR cc_start: 0.8875 (t) cc_final: 0.8431 (m) REVERT: A 62 LYS cc_start: 0.8259 (mttt) cc_final: 0.7468 (mtpt) REVERT: A 78 MET cc_start: 0.8595 (tpp) cc_final: 0.8117 (tpp) REVERT: A 82 MET cc_start: 0.7846 (mmm) cc_final: 0.7615 (mmm) REVERT: A 106 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7535 (ttmm) REVERT: A 233 TYR cc_start: 0.8074 (m-80) cc_final: 0.7727 (m-80) REVERT: A 242 LYS cc_start: 0.7482 (mttt) cc_final: 0.6964 (mmmt) REVERT: A 255 ASP cc_start: 0.8409 (p0) cc_final: 0.8111 (p0) REVERT: A 293 LYS cc_start: 0.7812 (tttp) cc_final: 0.7573 (tttt) REVERT: A 311 LYS cc_start: 0.8352 (tttp) cc_final: 0.8004 (tttt) REVERT: A 349 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7975 (mmtp) REVERT: A 394 THR cc_start: 0.8685 (m) cc_final: 0.8320 (t) REVERT: A 471 ILE cc_start: 0.8494 (mt) cc_final: 0.8285 (mm) REVERT: B 15 GLU cc_start: 0.6686 (pp20) cc_final: 0.6412 (pp20) REVERT: B 21 GLN cc_start: 0.8190 (tt0) cc_final: 0.7593 (tt0) REVERT: B 78 MET cc_start: 0.8639 (tpp) cc_final: 0.8116 (tpp) REVERT: B 106 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7484 (ttmm) REVERT: B 242 LYS cc_start: 0.7408 (mttt) cc_final: 0.7025 (mmtt) REVERT: B 255 ASP cc_start: 0.8324 (p0) cc_final: 0.8113 (p0) REVERT: B 293 LYS cc_start: 0.7831 (tttp) cc_final: 0.7594 (tttt) REVERT: B 311 LYS cc_start: 0.8347 (tttp) cc_final: 0.7913 (tttt) REVERT: B 394 THR cc_start: 0.8126 (m) cc_final: 0.7838 (t) REVERT: C 78 MET cc_start: 0.8468 (tpp) cc_final: 0.7986 (tpp) REVERT: C 82 MET cc_start: 0.7797 (mmm) cc_final: 0.7588 (mmm) REVERT: C 106 LYS cc_start: 0.7715 (ttmt) cc_final: 0.7478 (ttmm) REVERT: C 242 LYS cc_start: 0.7384 (mttt) cc_final: 0.7040 (mmmt) REVERT: C 255 ASP cc_start: 0.8328 (p0) cc_final: 0.8062 (p0) REVERT: C 277 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8571 (tm-30) REVERT: C 349 LYS cc_start: 0.8269 (mmtp) cc_final: 0.7966 (mmtt) REVERT: C 454 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7774 (mm-40) REVERT: D 60 THR cc_start: 0.8798 (t) cc_final: 0.8351 (m) REVERT: D 62 LYS cc_start: 0.8275 (mttt) cc_final: 0.7597 (mtpt) REVERT: D 75 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7256 (mt-10) REVERT: D 78 MET cc_start: 0.8454 (tpp) cc_final: 0.7975 (tpp) REVERT: D 82 MET cc_start: 0.7801 (mmm) cc_final: 0.7596 (mmm) REVERT: D 85 MET cc_start: 0.7415 (mmm) cc_final: 0.7148 (mmm) REVERT: D 106 LYS cc_start: 0.7649 (ttmt) cc_final: 0.7422 (ttmm) REVERT: D 233 TYR cc_start: 0.8160 (m-80) cc_final: 0.7767 (m-80) REVERT: D 242 LYS cc_start: 0.7471 (mttt) cc_final: 0.7031 (mmtt) REVERT: D 255 ASP cc_start: 0.8221 (p0) cc_final: 0.7988 (p0) REVERT: D 293 LYS cc_start: 0.7876 (tttp) cc_final: 0.7668 (tttt) REVERT: D 303 ASN cc_start: 0.8156 (m-40) cc_final: 0.7950 (m-40) REVERT: D 349 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7933 (mmtt) REVERT: D 454 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7571 (mm-40) REVERT: D 500 GLU cc_start: 0.6167 (tt0) cc_final: 0.5952 (tt0) REVERT: E 15 GLU cc_start: 0.6585 (pp20) cc_final: 0.6327 (pp20) REVERT: E 21 GLN cc_start: 0.8240 (tt0) cc_final: 0.8034 (tt0) REVERT: E 62 LYS cc_start: 0.8170 (mttt) cc_final: 0.7531 (mtpt) REVERT: E 78 MET cc_start: 0.8593 (tpp) cc_final: 0.7972 (tpp) REVERT: E 82 MET cc_start: 0.7818 (mmm) cc_final: 0.7595 (mmm) REVERT: E 106 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7454 (ttmm) REVERT: E 242 LYS cc_start: 0.7517 (mttt) cc_final: 0.6977 (mmmt) REVERT: E 255 ASP cc_start: 0.8357 (p0) cc_final: 0.8082 (p0) REVERT: E 293 LYS cc_start: 0.7769 (tttp) cc_final: 0.7486 (tttt) REVERT: E 349 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7887 (mmtp) REVERT: E 394 THR cc_start: 0.8661 (m) cc_final: 0.8290 (t) REVERT: E 470 ASP cc_start: 0.7738 (m-30) cc_final: 0.7438 (m-30) REVERT: F 28 ASP cc_start: 0.7352 (p0) cc_final: 0.6755 (p0) REVERT: F 62 LYS cc_start: 0.8263 (mttt) cc_final: 0.7505 (mtpt) REVERT: F 78 MET cc_start: 0.8571 (tpp) cc_final: 0.8049 (tpp) REVERT: F 82 MET cc_start: 0.7912 (mmm) cc_final: 0.7675 (mmm) REVERT: F 85 MET cc_start: 0.7717 (mmm) cc_final: 0.7434 (mmm) REVERT: F 242 LYS cc_start: 0.7515 (mttt) cc_final: 0.6990 (mmmt) REVERT: F 277 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8555 (tm-30) REVERT: F 293 LYS cc_start: 0.7779 (tttp) cc_final: 0.7516 (tttt) REVERT: F 311 LYS cc_start: 0.8335 (tttp) cc_final: 0.7882 (tttt) REVERT: F 349 LYS cc_start: 0.8301 (mmtp) cc_final: 0.7983 (mmtp) REVERT: F 394 THR cc_start: 0.8596 (m) cc_final: 0.8228 (t) REVERT: F 454 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7651 (mm-40) REVERT: F 495 MET cc_start: 0.7190 (mmm) cc_final: 0.6861 (mmm) REVERT: G 60 THR cc_start: 0.8859 (t) cc_final: 0.8350 (m) REVERT: G 78 MET cc_start: 0.8570 (tpp) cc_final: 0.8074 (tpp) REVERT: G 82 MET cc_start: 0.7813 (mmm) cc_final: 0.7596 (mmm) REVERT: G 85 MET cc_start: 0.7628 (mmm) cc_final: 0.7301 (mmm) REVERT: G 106 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7468 (ttmm) REVERT: G 109 LYS cc_start: 0.7732 (mttm) cc_final: 0.7522 (mmtt) REVERT: G 233 TYR cc_start: 0.7843 (m-80) cc_final: 0.7643 (m-80) REVERT: G 242 LYS cc_start: 0.7377 (mttt) cc_final: 0.6959 (mmtt) REVERT: G 293 LYS cc_start: 0.7852 (tttp) cc_final: 0.7637 (tttt) REVERT: G 311 LYS cc_start: 0.8346 (tttp) cc_final: 0.8107 (tttm) REVERT: G 394 THR cc_start: 0.8597 (m) cc_final: 0.8288 (t) REVERT: G 454 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7439 (mm-40) REVERT: G 470 ASP cc_start: 0.7785 (m-30) cc_final: 0.7511 (m-30) REVERT: H 21 GLN cc_start: 0.8159 (tt0) cc_final: 0.7774 (tt0) REVERT: H 62 LYS cc_start: 0.8304 (mttt) cc_final: 0.7618 (mtpt) REVERT: H 78 MET cc_start: 0.8569 (tpp) cc_final: 0.8004 (tpp) REVERT: H 82 MET cc_start: 0.7752 (mmm) cc_final: 0.7519 (mmm) REVERT: H 106 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7521 (ttmm) REVERT: H 109 LYS cc_start: 0.7805 (mttm) cc_final: 0.7579 (mmtt) REVERT: H 242 LYS cc_start: 0.7463 (mttt) cc_final: 0.6977 (mmmt) REVERT: H 349 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7966 (mmtt) REVERT: H 454 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7656 (mm-40) REVERT: H 470 ASP cc_start: 0.7857 (m-30) cc_final: 0.7557 (m-30) outliers start: 42 outliers final: 16 residues processed: 676 average time/residue: 1.3675 time to fit residues: 1054.3605 Evaluate side-chains 596 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 578 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain H residue 377 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN C 100 GLN C 312 ASN D 100 GLN D 312 ASN E 100 GLN F 100 GLN F 312 ASN G 100 GLN G 312 ASN H 100 GLN H 312 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126501 restraints weight = 66601.919| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.07 r_work: 0.3312 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20704 Z= 0.162 Angle : 0.633 5.967 27952 Z= 0.345 Chirality : 0.043 0.158 3240 Planarity : 0.004 0.032 3592 Dihedral : 6.322 47.075 2924 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.65 % Favored : 96.05 % Rotamer: Outliers : 1.87 % Allowed : 12.64 % Favored : 85.49 % 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: 0.18 (0.16), residues: 2632 helix: 1.12 (0.15), residues: 1176 sheet: -0.29 (0.28), residues: 216 loop : -0.75 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 253 TYR 0.013 0.002 TYR H 353 PHE 0.011 0.002 PHE G 24 HIS 0.004 0.001 HIS H 92 Details of bonding type rmsd covalent geometry : bond 0.00343 (20704) covalent geometry : angle 0.63306 (27952) hydrogen bonds : bond 0.05278 ( 962) hydrogen bonds : angle 6.29651 ( 2745) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 603 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7690 (p0) cc_final: 0.7402 (p0) REVERT: A 60 THR cc_start: 0.9060 (t) cc_final: 0.8681 (m) REVERT: A 62 LYS cc_start: 0.8708 (mttt) cc_final: 0.8308 (mtpt) REVERT: A 78 MET cc_start: 0.8812 (tpp) cc_final: 0.8412 (tpp) REVERT: A 94 ASN cc_start: 0.8337 (m110) cc_final: 0.7968 (t0) REVERT: A 106 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7866 (mtpt) REVERT: A 242 LYS cc_start: 0.7702 (mttt) cc_final: 0.7336 (mptt) REVERT: A 255 ASP cc_start: 0.8267 (p0) cc_final: 0.8051 (p0) REVERT: A 318 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8632 (m) REVERT: A 349 LYS cc_start: 0.8833 (mmtp) cc_final: 0.8560 (mmtt) REVERT: A 394 THR cc_start: 0.8956 (m) cc_final: 0.8725 (p) REVERT: B 1 MET cc_start: 0.6254 (tpt) cc_final: 0.5405 (tpp) REVERT: B 66 ILE cc_start: 0.9028 (mt) cc_final: 0.8788 (mm) REVERT: B 78 MET cc_start: 0.8866 (tpp) cc_final: 0.8474 (tpp) REVERT: B 94 ASN cc_start: 0.8294 (m110) cc_final: 0.7916 (t0) REVERT: B 241 GLN cc_start: 0.7917 (mt0) cc_final: 0.7696 (mt0) REVERT: B 242 LYS cc_start: 0.7717 (mttt) cc_final: 0.7513 (mmtt) REVERT: B 255 ASP cc_start: 0.8297 (p0) cc_final: 0.8064 (p0) REVERT: B 349 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8609 (mmtp) REVERT: B 394 THR cc_start: 0.8528 (m) cc_final: 0.8174 (t) REVERT: C 66 ILE cc_start: 0.8953 (mt) cc_final: 0.8744 (mm) REVERT: C 78 MET cc_start: 0.8815 (tpp) cc_final: 0.8338 (tpp) REVERT: C 82 MET cc_start: 0.8520 (mmm) cc_final: 0.8230 (mmm) REVERT: C 242 LYS cc_start: 0.7666 (mttt) cc_final: 0.7418 (mmtt) REVERT: C 255 ASP cc_start: 0.8289 (p0) cc_final: 0.8060 (p0) REVERT: C 349 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8592 (mmtt) REVERT: D 60 THR cc_start: 0.9099 (t) cc_final: 0.8667 (m) REVERT: D 62 LYS cc_start: 0.8760 (mttt) cc_final: 0.8384 (mtpt) REVERT: D 66 ILE cc_start: 0.8978 (mt) cc_final: 0.8754 (mm) REVERT: D 75 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7649 (mt-10) REVERT: D 78 MET cc_start: 0.8820 (tpp) cc_final: 0.8360 (tpp) REVERT: D 82 MET cc_start: 0.8472 (mmm) cc_final: 0.8187 (mmm) REVERT: D 106 LYS cc_start: 0.8034 (ttmt) cc_final: 0.7799 (mtpt) REVERT: D 233 TYR cc_start: 0.8542 (m-80) cc_final: 0.8251 (m-80) REVERT: D 242 LYS cc_start: 0.7783 (mttt) cc_final: 0.7448 (mmtt) REVERT: D 454 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7728 (mm-40) REVERT: D 495 MET cc_start: 0.7989 (tpt) cc_final: 0.7781 (tpt) REVERT: E 66 ILE cc_start: 0.8969 (mt) cc_final: 0.8746 (mm) REVERT: E 78 MET cc_start: 0.8837 (tpp) cc_final: 0.8474 (tpp) REVERT: E 242 LYS cc_start: 0.7750 (mttt) cc_final: 0.7353 (mmtt) REVERT: F 28 ASP cc_start: 0.7791 (p0) cc_final: 0.7390 (p0) REVERT: F 60 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8629 (m) REVERT: F 62 LYS cc_start: 0.8766 (mttt) cc_final: 0.8328 (mtpt) REVERT: F 78 MET cc_start: 0.8799 (tpp) cc_final: 0.8378 (tpp) REVERT: F 98 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7323 (mm-30) REVERT: F 242 LYS cc_start: 0.7779 (mttt) cc_final: 0.7368 (mmmt) REVERT: F 318 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8624 (m) REVERT: F 349 LYS cc_start: 0.8769 (mmtp) cc_final: 0.8552 (mmtp) REVERT: F 394 THR cc_start: 0.8906 (m) cc_final: 0.8650 (p) REVERT: F 470 ASP cc_start: 0.8396 (m-30) cc_final: 0.8117 (m-30) REVERT: G 60 THR cc_start: 0.9096 (t) cc_final: 0.8668 (m) REVERT: G 78 MET cc_start: 0.8800 (tpp) cc_final: 0.8468 (tpp) REVERT: G 242 LYS cc_start: 0.7687 (mttt) cc_final: 0.7363 (mmtt) REVERT: G 349 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8615 (mmtp) REVERT: G 394 THR cc_start: 0.8904 (m) cc_final: 0.8531 (t) REVERT: G 454 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7522 (mm-40) REVERT: H 28 ASP cc_start: 0.7678 (p0) cc_final: 0.7373 (p0) REVERT: H 66 ILE cc_start: 0.9041 (mt) cc_final: 0.8822 (mm) REVERT: H 78 MET cc_start: 0.8810 (tpp) cc_final: 0.8455 (tpp) REVERT: H 98 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7459 (mm-30) REVERT: H 242 LYS cc_start: 0.7673 (mttt) cc_final: 0.7366 (mmtt) REVERT: H 337 MET cc_start: 0.5781 (pmt) cc_final: 0.5505 (pmt) REVERT: H 349 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8594 (mmtt) REVERT: H 454 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7747 (mm-40) outliers start: 40 outliers final: 17 residues processed: 633 average time/residue: 1.2968 time to fit residues: 938.8226 Evaluate side-chains 567 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 547 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 377 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 62 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN G 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126042 restraints weight = 66291.584| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.05 r_work: 0.3279 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20704 Z= 0.184 Angle : 0.592 6.124 27952 Z= 0.317 Chirality : 0.043 0.147 3240 Planarity : 0.004 0.035 3592 Dihedral : 5.320 39.405 2903 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.95 % Favored : 95.74 % Rotamer: Outliers : 2.62 % Allowed : 13.44 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.16), residues: 2632 helix: 1.58 (0.15), residues: 1176 sheet: -1.08 (0.27), residues: 264 loop : -0.67 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 253 TYR 0.013 0.002 TYR H 353 PHE 0.012 0.002 PHE F 110 HIS 0.004 0.001 HIS H -20 Details of bonding type rmsd covalent geometry : bond 0.00427 (20704) covalent geometry : angle 0.59188 (27952) hydrogen bonds : bond 0.04959 ( 962) hydrogen bonds : angle 5.86245 ( 2745) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 539 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7653 (p0) cc_final: 0.7369 (p0) REVERT: A 60 THR cc_start: 0.9089 (t) cc_final: 0.8741 (m) REVERT: A 78 MET cc_start: 0.8798 (tpp) cc_final: 0.8426 (tpp) REVERT: A 94 ASN cc_start: 0.8378 (m110) cc_final: 0.8016 (t0) REVERT: A 349 LYS cc_start: 0.8886 (mmtp) cc_final: 0.8611 (mmtt) REVERT: A 394 THR cc_start: 0.9032 (m) cc_final: 0.8797 (p) REVERT: A 454 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7664 (mm110) REVERT: A 495 MET cc_start: 0.8205 (tpt) cc_final: 0.7894 (mmt) REVERT: B 60 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8648 (m) REVERT: B 66 ILE cc_start: 0.9078 (mt) cc_final: 0.8836 (mm) REVERT: B 78 MET cc_start: 0.8805 (tpp) cc_final: 0.8533 (tpp) REVERT: B 94 ASN cc_start: 0.8287 (m110) cc_final: 0.7969 (t0) REVERT: B 241 GLN cc_start: 0.8034 (mt0) cc_final: 0.7789 (mt0) REVERT: B 242 LYS cc_start: 0.7854 (mttt) cc_final: 0.7585 (mmtt) REVERT: B 349 LYS cc_start: 0.8903 (mmtp) cc_final: 0.8700 (mmtp) REVERT: B 394 THR cc_start: 0.8771 (m) cc_final: 0.8440 (t) REVERT: C 60 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8660 (m) REVERT: C 78 MET cc_start: 0.8792 (tpp) cc_final: 0.8463 (tpp) REVERT: C 242 LYS cc_start: 0.7824 (mttt) cc_final: 0.7560 (mmtt) REVERT: C 274 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: C 322 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.7906 (ttm170) REVERT: C 454 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7922 (mm110) REVERT: D 48 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7681 (mt-10) REVERT: D 60 THR cc_start: 0.9136 (t) cc_final: 0.8729 (m) REVERT: D 66 ILE cc_start: 0.9014 (mt) cc_final: 0.8799 (mm) REVERT: D 75 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7542 (mt-10) REVERT: D 78 MET cc_start: 0.8731 (tpp) cc_final: 0.8376 (tpp) REVERT: D 233 TYR cc_start: 0.8565 (m-80) cc_final: 0.8288 (m-80) REVERT: D 242 LYS cc_start: 0.7913 (mttt) cc_final: 0.7557 (mmmt) REVERT: E 1 MET cc_start: 0.6789 (tpp) cc_final: 0.6584 (tpp) REVERT: E 28 ASP cc_start: 0.7641 (p0) cc_final: 0.7350 (p0) REVERT: E 60 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8652 (m) REVERT: E 78 MET cc_start: 0.8822 (tpp) cc_final: 0.8532 (tpp) REVERT: E 242 LYS cc_start: 0.7867 (mttt) cc_final: 0.7492 (mmtt) REVERT: F 60 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8734 (m) REVERT: F 78 MET cc_start: 0.8778 (tpp) cc_final: 0.8482 (tpp) REVERT: F 82 MET cc_start: 0.8240 (mmm) cc_final: 0.7962 (mmm) REVERT: F 98 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7471 (mm-30) REVERT: F 242 LYS cc_start: 0.7931 (mttt) cc_final: 0.7516 (mmtt) REVERT: F 274 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: F 349 LYS cc_start: 0.8887 (mmtp) cc_final: 0.8602 (mmtt) REVERT: F 394 THR cc_start: 0.8977 (m) cc_final: 0.8715 (p) REVERT: G 60 THR cc_start: 0.9128 (t) cc_final: 0.8730 (m) REVERT: G 66 ILE cc_start: 0.9096 (mt) cc_final: 0.8877 (mm) REVERT: G 78 MET cc_start: 0.8794 (tpp) cc_final: 0.8491 (tpp) REVERT: G 242 LYS cc_start: 0.7846 (mttt) cc_final: 0.7495 (mmtt) REVERT: G 335 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.4576 (mp0) REVERT: G 394 THR cc_start: 0.8983 (m) cc_final: 0.8718 (p) REVERT: H 60 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8636 (m) REVERT: H 62 LYS cc_start: 0.8710 (mttp) cc_final: 0.8192 (mtpt) REVERT: H 66 ILE cc_start: 0.9056 (mt) cc_final: 0.8814 (mm) REVERT: H 78 MET cc_start: 0.8765 (tpp) cc_final: 0.8445 (tpp) REVERT: H 98 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7506 (mm-30) REVERT: H 242 LYS cc_start: 0.7830 (mttt) cc_final: 0.7468 (mmmt) REVERT: H 337 MET cc_start: 0.5931 (pmt) cc_final: 0.5714 (pmt) REVERT: H 349 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8626 (mmtt) REVERT: H 394 THR cc_start: 0.8875 (m) cc_final: 0.8402 (t) outliers start: 56 outliers final: 25 residues processed: 578 average time/residue: 1.3704 time to fit residues: 901.7337 Evaluate side-chains 549 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 515 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 209 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN C 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126916 restraints weight = 66195.635| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.07 r_work: 0.3291 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20704 Z= 0.153 Angle : 0.547 6.209 27952 Z= 0.290 Chirality : 0.041 0.144 3240 Planarity : 0.004 0.041 3592 Dihedral : 4.938 39.422 2899 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.80 % Favored : 95.90 % Rotamer: Outliers : 2.62 % Allowed : 15.64 % Favored : 81.74 % 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: 0.86 (0.17), residues: 2632 helix: 1.97 (0.16), residues: 1184 sheet: -0.97 (0.27), residues: 264 loop : -0.48 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 253 TYR 0.013 0.001 TYR A 353 PHE 0.009 0.001 PHE E 24 HIS 0.004 0.001 HIS H -20 Details of bonding type rmsd covalent geometry : bond 0.00354 (20704) covalent geometry : angle 0.54725 (27952) hydrogen bonds : bond 0.04312 ( 962) hydrogen bonds : angle 5.61656 ( 2745) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 550 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7659 (p0) cc_final: 0.7357 (p0) REVERT: A 60 THR cc_start: 0.9096 (t) cc_final: 0.8742 (m) REVERT: A 78 MET cc_start: 0.8813 (tpp) cc_final: 0.8412 (tpp) REVERT: A 94 ASN cc_start: 0.8369 (m110) cc_final: 0.8043 (t0) REVERT: A 337 MET cc_start: 0.5893 (pmt) cc_final: 0.5604 (pmt) REVERT: A 349 LYS cc_start: 0.8912 (mmtp) cc_final: 0.8646 (mmtt) REVERT: A 394 THR cc_start: 0.9018 (m) cc_final: 0.8788 (p) REVERT: A 454 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7596 (mm110) REVERT: B 60 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8664 (m) REVERT: B 66 ILE cc_start: 0.9112 (mt) cc_final: 0.8878 (mm) REVERT: B 78 MET cc_start: 0.8732 (tpp) cc_final: 0.8341 (tpp) REVERT: B 94 ASN cc_start: 0.8326 (m110) cc_final: 0.8000 (t0) REVERT: B 242 LYS cc_start: 0.7836 (mttt) cc_final: 0.7512 (mmmt) REVERT: B 394 THR cc_start: 0.8827 (m) cc_final: 0.8485 (t) REVERT: C 28 ASP cc_start: 0.7657 (p0) cc_final: 0.7201 (p0) REVERT: C 60 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8683 (m) REVERT: C 78 MET cc_start: 0.8748 (tpp) cc_final: 0.8451 (tpp) REVERT: C 242 LYS cc_start: 0.7860 (mttt) cc_final: 0.7575 (mmtt) REVERT: C 318 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8677 (m) REVERT: C 454 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7894 (mm110) REVERT: D 28 ASP cc_start: 0.7369 (p0) cc_final: 0.6971 (p0) REVERT: D 48 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7685 (mt-10) REVERT: D 60 THR cc_start: 0.9144 (t) cc_final: 0.8733 (m) REVERT: D 233 TYR cc_start: 0.8525 (m-80) cc_final: 0.8279 (m-80) REVERT: D 242 LYS cc_start: 0.7886 (mttt) cc_final: 0.7515 (mmmt) REVERT: D 454 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7760 (mm110) REVERT: E 60 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8657 (m) REVERT: E 78 MET cc_start: 0.8785 (tpp) cc_final: 0.8389 (tpp) REVERT: E 242 LYS cc_start: 0.7884 (mttt) cc_final: 0.7498 (mmtt) REVERT: F 60 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8757 (m) REVERT: F 78 MET cc_start: 0.8735 (tpp) cc_final: 0.8492 (tpp) REVERT: F 82 MET cc_start: 0.8302 (mmm) cc_final: 0.8058 (mmm) REVERT: F 98 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7535 (mm-30) REVERT: F 242 LYS cc_start: 0.7947 (mttt) cc_final: 0.7529 (mmtt) REVERT: F 394 THR cc_start: 0.8992 (m) cc_final: 0.8730 (p) REVERT: G 28 ASP cc_start: 0.7308 (p0) cc_final: 0.7038 (p0) REVERT: G 43 ASP cc_start: 0.8380 (p0) cc_final: 0.8162 (p0) REVERT: G 60 THR cc_start: 0.9140 (t) cc_final: 0.8740 (m) REVERT: G 62 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8247 (mmmt) REVERT: G 66 ILE cc_start: 0.9128 (mt) cc_final: 0.8926 (mm) REVERT: G 78 MET cc_start: 0.8771 (tpp) cc_final: 0.8449 (tpp) REVERT: G 242 LYS cc_start: 0.7772 (mttt) cc_final: 0.7423 (mmmt) REVERT: G 335 GLU cc_start: 0.5609 (OUTLIER) cc_final: 0.4901 (mp0) REVERT: G 394 THR cc_start: 0.8977 (m) cc_final: 0.8718 (p) REVERT: H 28 ASP cc_start: 0.7536 (p0) cc_final: 0.7256 (p0) REVERT: H 60 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8643 (m) REVERT: H 66 ILE cc_start: 0.9099 (mt) cc_final: 0.8856 (mm) REVERT: H 78 MET cc_start: 0.8698 (tpp) cc_final: 0.8399 (tpp) REVERT: H 98 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7507 (mm-30) REVERT: H 242 LYS cc_start: 0.7843 (mttt) cc_final: 0.7518 (mmtt) REVERT: H 337 MET cc_start: 0.5863 (pmt) cc_final: 0.5640 (pmt) REVERT: H 349 LYS cc_start: 0.8909 (mmtp) cc_final: 0.8651 (mmtt) outliers start: 56 outliers final: 28 residues processed: 588 average time/residue: 1.3589 time to fit residues: 909.1421 Evaluate side-chains 565 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 530 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 21 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN B 343 GLN C 343 GLN D 343 GLN E 312 ASN E 343 GLN E 454 GLN F 343 GLN G 343 GLN G 454 GLN H 343 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125939 restraints weight = 66105.824| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.06 r_work: 0.3280 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20704 Z= 0.187 Angle : 0.563 6.310 27952 Z= 0.300 Chirality : 0.042 0.144 3240 Planarity : 0.004 0.034 3592 Dihedral : 4.835 19.763 2896 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.07 % Favored : 95.63 % Rotamer: Outliers : 2.62 % Allowed : 16.67 % Favored : 80.71 % 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: 0.82 (0.17), residues: 2632 helix: 1.92 (0.16), residues: 1184 sheet: -0.89 (0.27), residues: 264 loop : -0.51 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 253 TYR 0.013 0.002 TYR B 282 PHE 0.012 0.001 PHE F 110 HIS 0.004 0.001 HIS G 296 Details of bonding type rmsd covalent geometry : bond 0.00437 (20704) covalent geometry : angle 0.56342 (27952) hydrogen bonds : bond 0.04632 ( 962) hydrogen bonds : angle 5.56807 ( 2745) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 539 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7670 (p0) cc_final: 0.7359 (p0) REVERT: A 60 THR cc_start: 0.9133 (t) cc_final: 0.8781 (m) REVERT: A 78 MET cc_start: 0.8748 (tpp) cc_final: 0.8330 (tpp) REVERT: A 94 ASN cc_start: 0.8382 (m110) cc_final: 0.8050 (t0) REVERT: A 337 MET cc_start: 0.5913 (pmt) cc_final: 0.5679 (pmt) REVERT: A 349 LYS cc_start: 0.8928 (mmtp) cc_final: 0.8663 (mmtt) REVERT: A 394 THR cc_start: 0.8999 (m) cc_final: 0.8747 (p) REVERT: A 454 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7714 (mm110) REVERT: B 60 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8728 (m) REVERT: B 62 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8332 (mmmm) REVERT: B 66 ILE cc_start: 0.9121 (mt) cc_final: 0.8896 (mm) REVERT: B 78 MET cc_start: 0.8754 (tpp) cc_final: 0.8384 (tpp) REVERT: B 94 ASN cc_start: 0.8300 (m110) cc_final: 0.7983 (t0) REVERT: B 242 LYS cc_start: 0.7891 (mttt) cc_final: 0.7617 (mmmt) REVERT: B 394 THR cc_start: 0.8881 (m) cc_final: 0.8513 (t) REVERT: C 28 ASP cc_start: 0.7497 (p0) cc_final: 0.7205 (p0) REVERT: C 60 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8723 (m) REVERT: C 62 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8340 (mmmm) REVERT: C 78 MET cc_start: 0.8689 (tpp) cc_final: 0.8344 (tpp) REVERT: C 242 LYS cc_start: 0.7908 (mttt) cc_final: 0.7662 (mmtt) REVERT: D 28 ASP cc_start: 0.7404 (p0) cc_final: 0.7057 (p0) REVERT: D 48 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7709 (mt-10) REVERT: D 60 THR cc_start: 0.9137 (t) cc_final: 0.8729 (m) REVERT: D 62 LYS cc_start: 0.8656 (mttp) cc_final: 0.8225 (mmmt) REVERT: D 242 LYS cc_start: 0.7954 (mttt) cc_final: 0.7630 (mmmt) REVERT: D 454 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7726 (mm110) REVERT: D 500 GLU cc_start: 0.6732 (tt0) cc_final: 0.6236 (pt0) REVERT: E 60 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8680 (m) REVERT: E 62 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8358 (mmmm) REVERT: E 78 MET cc_start: 0.8777 (tpp) cc_final: 0.8554 (tpp) REVERT: E 242 LYS cc_start: 0.7907 (mttt) cc_final: 0.7570 (mmtt) REVERT: E 322 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.7967 (ttm170) REVERT: E 454 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.6821 (mm-40) REVERT: F 60 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8771 (m) REVERT: F 78 MET cc_start: 0.8735 (tpp) cc_final: 0.8395 (tpp) REVERT: F 82 MET cc_start: 0.8272 (mmm) cc_final: 0.8042 (mmm) REVERT: F 98 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7477 (mm-30) REVERT: F 242 LYS cc_start: 0.7951 (mttt) cc_final: 0.7587 (mmtt) REVERT: F 277 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.6274 (tm-30) REVERT: F 335 GLU cc_start: 0.5523 (OUTLIER) cc_final: 0.4894 (mp0) REVERT: F 394 THR cc_start: 0.8993 (m) cc_final: 0.8724 (p) REVERT: G 60 THR cc_start: 0.9125 (t) cc_final: 0.8735 (m) REVERT: G 62 LYS cc_start: 0.8643 (mmtp) cc_final: 0.8276 (mmmm) REVERT: G 78 MET cc_start: 0.8742 (tpp) cc_final: 0.8414 (tpp) REVERT: G 242 LYS cc_start: 0.7942 (mttt) cc_final: 0.7572 (mmmt) REVERT: G 335 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.5005 (mp0) REVERT: G 394 THR cc_start: 0.8977 (m) cc_final: 0.8725 (p) REVERT: G 454 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7619 (mm110) REVERT: H 28 ASP cc_start: 0.7358 (p0) cc_final: 0.7099 (p0) REVERT: H 60 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8679 (m) REVERT: H 98 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7571 (mm-30) REVERT: H 242 LYS cc_start: 0.7876 (mttt) cc_final: 0.7544 (mmtt) REVERT: H 322 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.7931 (ttm170) REVERT: H 349 LYS cc_start: 0.8903 (mmtp) cc_final: 0.8633 (mmtt) REVERT: H 454 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7764 (mm110) outliers start: 56 outliers final: 33 residues processed: 579 average time/residue: 1.3347 time to fit residues: 879.3984 Evaluate side-chains 567 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 522 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 322 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 260 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN B 21 GLN B 343 GLN C 241 GLN C 343 GLN D 343 GLN E 343 GLN F 241 GLN F 343 GLN F 454 GLN G 343 GLN H 343 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.157279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126667 restraints weight = 66093.222| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.07 r_work: 0.3297 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20704 Z= 0.158 Angle : 0.551 8.038 27952 Z= 0.290 Chirality : 0.042 0.151 3240 Planarity : 0.004 0.034 3592 Dihedral : 4.764 20.249 2896 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.76 % Favored : 95.93 % Rotamer: Outliers : 2.43 % Allowed : 17.37 % Favored : 80.20 % 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: 0.96 (0.17), residues: 2632 helix: 2.06 (0.16), residues: 1184 sheet: -0.81 (0.27), residues: 264 loop : -0.45 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 253 TYR 0.012 0.001 TYR C 353 PHE 0.008 0.001 PHE H 110 HIS 0.003 0.001 HIS H -20 Details of bonding type rmsd covalent geometry : bond 0.00369 (20704) covalent geometry : angle 0.55116 (27952) hydrogen bonds : bond 0.04318 ( 962) hydrogen bonds : angle 5.48188 ( 2745) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 531 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7689 (p0) cc_final: 0.7398 (p0) REVERT: A 60 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8784 (m) REVERT: A 94 ASN cc_start: 0.8395 (m110) cc_final: 0.8087 (t0) REVERT: A 337 MET cc_start: 0.5863 (pmt) cc_final: 0.5655 (pmt) REVERT: A 349 LYS cc_start: 0.8926 (mmtp) cc_final: 0.8660 (mmtt) REVERT: A 394 THR cc_start: 0.9000 (m) cc_final: 0.8755 (p) REVERT: A 454 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7691 (mm110) REVERT: B 60 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8735 (m) REVERT: B 62 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8331 (mmmm) REVERT: B 66 ILE cc_start: 0.9124 (mt) cc_final: 0.8901 (mm) REVERT: B 78 MET cc_start: 0.8737 (tpp) cc_final: 0.8374 (tpp) REVERT: B 94 ASN cc_start: 0.8260 (m110) cc_final: 0.7952 (t0) REVERT: B 242 LYS cc_start: 0.7873 (mttt) cc_final: 0.7618 (mmmt) REVERT: B 394 THR cc_start: 0.8859 (m) cc_final: 0.8491 (t) REVERT: C 28 ASP cc_start: 0.7457 (p0) cc_final: 0.7155 (p0) REVERT: C 60 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8733 (m) REVERT: C 62 LYS cc_start: 0.8678 (mmtp) cc_final: 0.8323 (mmmm) REVERT: C 78 MET cc_start: 0.8655 (tpp) cc_final: 0.8311 (tpp) REVERT: C 242 LYS cc_start: 0.7904 (mttt) cc_final: 0.7630 (mmmt) REVERT: C 500 GLU cc_start: 0.6887 (tt0) cc_final: 0.6549 (pt0) REVERT: D 28 ASP cc_start: 0.7373 (p0) cc_final: 0.7094 (p0) REVERT: D 48 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7714 (mt-10) REVERT: D 60 THR cc_start: 0.9145 (t) cc_final: 0.8730 (m) REVERT: D 62 LYS cc_start: 0.8635 (mttp) cc_final: 0.8210 (mmmt) REVERT: D 242 LYS cc_start: 0.7959 (mttt) cc_final: 0.7640 (mmmt) REVERT: D 322 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7940 (ttm170) REVERT: D 454 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7810 (mm110) REVERT: D 500 GLU cc_start: 0.6688 (tt0) cc_final: 0.6297 (pt0) REVERT: E 28 ASP cc_start: 0.7622 (p0) cc_final: 0.7143 (p0) REVERT: E 60 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8697 (m) REVERT: E 62 LYS cc_start: 0.8690 (mmtm) cc_final: 0.8361 (mmmm) REVERT: E 78 MET cc_start: 0.8730 (tpp) cc_final: 0.8514 (tpp) REVERT: E 242 LYS cc_start: 0.7888 (mttt) cc_final: 0.7556 (mmtt) REVERT: E 277 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.6229 (tm-30) REVERT: F 60 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8780 (m) REVERT: F 62 LYS cc_start: 0.8635 (mttt) cc_final: 0.8291 (mmmm) REVERT: F 78 MET cc_start: 0.8701 (tpp) cc_final: 0.8354 (tpp) REVERT: F 82 MET cc_start: 0.8262 (mmm) cc_final: 0.8026 (mmm) REVERT: F 98 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7510 (mm-30) REVERT: F 242 LYS cc_start: 0.7955 (mttt) cc_final: 0.7597 (mmtt) REVERT: F 274 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: F 277 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.6326 (tm-30) REVERT: F 335 GLU cc_start: 0.5511 (OUTLIER) cc_final: 0.4945 (mp0) REVERT: F 394 THR cc_start: 0.8989 (m) cc_final: 0.8727 (p) REVERT: G 60 THR cc_start: 0.9116 (t) cc_final: 0.8740 (m) REVERT: G 62 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8287 (mmmm) REVERT: G 78 MET cc_start: 0.8714 (tpp) cc_final: 0.8387 (tpp) REVERT: G 233 TYR cc_start: 0.8155 (m-80) cc_final: 0.7929 (m-80) REVERT: G 242 LYS cc_start: 0.7929 (mttt) cc_final: 0.7578 (mmmt) REVERT: G 335 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.4936 (mp0) REVERT: G 394 THR cc_start: 0.8978 (m) cc_final: 0.8737 (p) REVERT: H 28 ASP cc_start: 0.7361 (p0) cc_final: 0.7093 (p0) REVERT: H 60 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8664 (m) REVERT: H 85 MET cc_start: 0.8170 (mmm) cc_final: 0.7938 (mmm) REVERT: H 98 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7533 (mm-30) REVERT: H 242 LYS cc_start: 0.7865 (mttt) cc_final: 0.7543 (mmtt) REVERT: H 322 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7926 (ttm170) REVERT: H 349 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8642 (mmtt) REVERT: H 454 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7804 (mm110) outliers start: 52 outliers final: 32 residues processed: 567 average time/residue: 1.3029 time to fit residues: 840.8336 Evaluate side-chains 563 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 518 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 454 GLN Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 322 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 190 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 229 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN B 21 GLN B 343 GLN C 343 GLN D 241 GLN D 343 GLN E 343 GLN E 454 GLN F 343 GLN G 343 GLN H 343 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.157220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126652 restraints weight = 66051.014| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.06 r_work: 0.3287 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20704 Z= 0.166 Angle : 0.557 8.152 27952 Z= 0.293 Chirality : 0.042 0.147 3240 Planarity : 0.004 0.035 3592 Dihedral : 4.736 19.655 2896 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.84 % Favored : 95.86 % Rotamer: Outliers : 2.67 % Allowed : 17.46 % Favored : 79.87 % 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: 0.96 (0.17), residues: 2632 helix: 2.06 (0.16), residues: 1184 sheet: -0.79 (0.27), residues: 264 loop : -0.46 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 253 TYR 0.012 0.001 TYR B 353 PHE 0.010 0.001 PHE C 110 HIS 0.003 0.001 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00389 (20704) covalent geometry : angle 0.55659 (27952) hydrogen bonds : bond 0.04341 ( 962) hydrogen bonds : angle 5.45102 ( 2745) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 530 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7679 (p0) cc_final: 0.7395 (p0) REVERT: A 60 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8786 (m) REVERT: A 78 MET cc_start: 0.8577 (tpp) cc_final: 0.8332 (tpp) REVERT: A 94 ASN cc_start: 0.8396 (m110) cc_final: 0.8082 (t0) REVERT: A 349 LYS cc_start: 0.8949 (mmtp) cc_final: 0.8687 (mmtt) REVERT: A 394 THR cc_start: 0.9000 (m) cc_final: 0.8750 (p) REVERT: A 454 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7636 (mm110) REVERT: B 60 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8733 (m) REVERT: B 62 LYS cc_start: 0.8706 (mmtp) cc_final: 0.8316 (mmmm) REVERT: B 66 ILE cc_start: 0.9131 (mt) cc_final: 0.8912 (mm) REVERT: B 94 ASN cc_start: 0.8316 (m110) cc_final: 0.8018 (t0) REVERT: B 242 LYS cc_start: 0.7897 (mttt) cc_final: 0.7613 (mmmt) REVERT: B 394 THR cc_start: 0.8880 (m) cc_final: 0.8492 (t) REVERT: C 28 ASP cc_start: 0.7369 (p0) cc_final: 0.7127 (p0) REVERT: C 60 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8747 (m) REVERT: C 62 LYS cc_start: 0.8673 (mmtp) cc_final: 0.8307 (mmmm) REVERT: C 78 MET cc_start: 0.8636 (tpp) cc_final: 0.8306 (tpp) REVERT: C 242 LYS cc_start: 0.7862 (mttt) cc_final: 0.7612 (mmmt) REVERT: C 500 GLU cc_start: 0.6850 (tt0) cc_final: 0.6560 (pt0) REVERT: D 28 ASP cc_start: 0.7360 (p0) cc_final: 0.7096 (p0) REVERT: D 48 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7745 (mt-10) REVERT: D 60 THR cc_start: 0.9150 (t) cc_final: 0.8730 (m) REVERT: D 62 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8222 (mmmt) REVERT: D 242 LYS cc_start: 0.7976 (mttt) cc_final: 0.7630 (mmmt) REVERT: D 322 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7939 (ttm170) REVERT: D 454 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7727 (mm110) REVERT: D 500 GLU cc_start: 0.6720 (tt0) cc_final: 0.6350 (pt0) REVERT: E 60 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8734 (m) REVERT: E 62 LYS cc_start: 0.8687 (mmtm) cc_final: 0.8356 (mmmm) REVERT: E 78 MET cc_start: 0.8697 (tpp) cc_final: 0.8495 (tpp) REVERT: E 242 LYS cc_start: 0.7888 (mttt) cc_final: 0.7572 (mmtt) REVERT: E 277 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.6291 (tm-30) REVERT: E 322 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.7999 (ttm170) REVERT: E 500 GLU cc_start: 0.6622 (tt0) cc_final: 0.6334 (pt0) REVERT: F 60 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8780 (m) REVERT: F 62 LYS cc_start: 0.8648 (mttt) cc_final: 0.8295 (mmmm) REVERT: F 78 MET cc_start: 0.8705 (tpp) cc_final: 0.8359 (tpp) REVERT: F 82 MET cc_start: 0.8261 (mmm) cc_final: 0.8032 (mmm) REVERT: F 98 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7592 (mm-30) REVERT: F 233 TYR cc_start: 0.8257 (m-80) cc_final: 0.7969 (m-80) REVERT: F 242 LYS cc_start: 0.7933 (mttt) cc_final: 0.7536 (mmmt) REVERT: F 274 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: F 277 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.6332 (tm-30) REVERT: F 337 MET cc_start: 0.5051 (pmm) cc_final: 0.4476 (pmt) REVERT: F 394 THR cc_start: 0.8986 (m) cc_final: 0.8721 (p) REVERT: G 60 THR cc_start: 0.9118 (t) cc_final: 0.8749 (m) REVERT: G 62 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8288 (mmmm) REVERT: G 78 MET cc_start: 0.8702 (tpp) cc_final: 0.8319 (tpp) REVERT: G 242 LYS cc_start: 0.7937 (mttt) cc_final: 0.7565 (mmmt) REVERT: G 277 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.6175 (tm-30) REVERT: G 335 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.4975 (mp0) REVERT: G 394 THR cc_start: 0.8981 (m) cc_final: 0.8747 (p) REVERT: H 28 ASP cc_start: 0.7305 (p0) cc_final: 0.7082 (p0) REVERT: H 60 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8674 (m) REVERT: H 94 ASN cc_start: 0.8295 (m-40) cc_final: 0.8078 (t0) REVERT: H 98 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7545 (mm-30) REVERT: H 277 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.6398 (tm-30) REVERT: H 322 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.7937 (ttm170) REVERT: H 349 LYS cc_start: 0.8933 (mmtp) cc_final: 0.8670 (mmtt) REVERT: H 454 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7778 (mm110) outliers start: 57 outliers final: 35 residues processed: 569 average time/residue: 1.3130 time to fit residues: 851.0982 Evaluate side-chains 568 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 517 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 322 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 181 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN B 343 GLN C 241 GLN C 343 GLN D 241 GLN D 343 GLN E 343 GLN E 454 GLN F 241 GLN F 343 GLN G 343 GLN G 454 GLN H 343 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126975 restraints weight = 65655.709| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.07 r_work: 0.3267 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20704 Z= 0.157 Angle : 0.552 7.149 27952 Z= 0.289 Chirality : 0.041 0.144 3240 Planarity : 0.004 0.035 3592 Dihedral : 4.692 19.723 2896 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.72 % Favored : 95.97 % Rotamer: Outliers : 2.57 % Allowed : 17.98 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.04 (0.17), residues: 2632 helix: 2.12 (0.16), residues: 1184 sheet: -0.76 (0.26), residues: 264 loop : -0.42 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 253 TYR 0.012 0.001 TYR C 353 PHE 0.009 0.001 PHE C 110 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00368 (20704) covalent geometry : angle 0.55162 (27952) hydrogen bonds : bond 0.04254 ( 962) hydrogen bonds : angle 5.40515 ( 2745) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 531 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8787 (m) REVERT: A 62 LYS cc_start: 0.8682 (mttp) cc_final: 0.8251 (mmmt) REVERT: A 94 ASN cc_start: 0.8392 (m110) cc_final: 0.8079 (t0) REVERT: A 349 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8672 (mmtt) REVERT: A 394 THR cc_start: 0.8955 (m) cc_final: 0.8713 (p) REVERT: A 454 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7613 (mm110) REVERT: B 60 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8735 (m) REVERT: B 62 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8299 (mmmm) REVERT: B 66 ILE cc_start: 0.9132 (mt) cc_final: 0.8906 (mm) REVERT: B 94 ASN cc_start: 0.8297 (m110) cc_final: 0.7994 (t0) REVERT: B 242 LYS cc_start: 0.7849 (mttt) cc_final: 0.7579 (mmmt) REVERT: B 394 THR cc_start: 0.8877 (m) cc_final: 0.8489 (t) REVERT: C 28 ASP cc_start: 0.7354 (p0) cc_final: 0.7142 (p0) REVERT: C 60 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8740 (m) REVERT: C 62 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8320 (mmmm) REVERT: C 242 LYS cc_start: 0.7921 (mttt) cc_final: 0.7617 (mmmt) REVERT: C 500 GLU cc_start: 0.6805 (tt0) cc_final: 0.6489 (pt0) REVERT: D 21 GLN cc_start: 0.8615 (mt0) cc_final: 0.8413 (mt0) REVERT: D 60 THR cc_start: 0.9150 (t) cc_final: 0.8734 (m) REVERT: D 62 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8258 (mmmm) REVERT: D 85 MET cc_start: 0.8038 (mmm) cc_final: 0.7827 (mmm) REVERT: D 242 LYS cc_start: 0.7962 (mttt) cc_final: 0.7627 (mmmt) REVERT: D 322 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7934 (ttm170) REVERT: D 454 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7836 (mm110) REVERT: D 500 GLU cc_start: 0.6708 (tt0) cc_final: 0.6445 (pt0) REVERT: E 28 ASP cc_start: 0.7631 (p0) cc_final: 0.7188 (p0) REVERT: E 60 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8732 (m) REVERT: E 62 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8322 (mmmm) REVERT: E 242 LYS cc_start: 0.7933 (mttt) cc_final: 0.7573 (mmmt) REVERT: E 277 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.6212 (tm-30) REVERT: E 322 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7997 (ttm170) REVERT: E 454 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: E 500 GLU cc_start: 0.6603 (tt0) cc_final: 0.6315 (pt0) REVERT: F 60 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8784 (m) REVERT: F 62 LYS cc_start: 0.8654 (mttt) cc_final: 0.8299 (mmmm) REVERT: F 78 MET cc_start: 0.8670 (tpp) cc_final: 0.8316 (tpp) REVERT: F 82 MET cc_start: 0.8260 (mmm) cc_final: 0.8032 (mmm) REVERT: F 94 ASN cc_start: 0.8281 (m110) cc_final: 0.7917 (t0) REVERT: F 98 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7589 (mm-30) REVERT: F 242 LYS cc_start: 0.7951 (mttt) cc_final: 0.7545 (mmmt) REVERT: F 277 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: F 337 MET cc_start: 0.5252 (pmm) cc_final: 0.4685 (pmt) REVERT: F 394 THR cc_start: 0.8981 (m) cc_final: 0.8714 (p) REVERT: G 60 THR cc_start: 0.9115 (t) cc_final: 0.8748 (m) REVERT: G 62 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8263 (mmmm) REVERT: G 78 MET cc_start: 0.8674 (tpp) cc_final: 0.8289 (tpp) REVERT: G 242 LYS cc_start: 0.7874 (mttt) cc_final: 0.7535 (mmmt) REVERT: G 277 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.6149 (tm-30) REVERT: G 335 GLU cc_start: 0.5477 (OUTLIER) cc_final: 0.5036 (mp0) REVERT: G 394 THR cc_start: 0.8972 (m) cc_final: 0.8733 (p) REVERT: G 454 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7469 (mm-40) REVERT: H 28 ASP cc_start: 0.7347 (p0) cc_final: 0.7141 (p0) REVERT: H 60 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8691 (m) REVERT: H 94 ASN cc_start: 0.8276 (m-40) cc_final: 0.8067 (t0) REVERT: H 98 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7594 (mm-30) REVERT: H 322 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.7925 (ttm170) REVERT: H 349 LYS cc_start: 0.8928 (mmtp) cc_final: 0.8657 (mmtt) REVERT: H 454 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7717 (mm110) outliers start: 55 outliers final: 36 residues processed: 571 average time/residue: 1.3026 time to fit residues: 849.2714 Evaluate side-chains 571 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 520 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 322 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 259 optimal weight: 0.5980 chunk 135 optimal weight: 0.7980 chunk 255 optimal weight: 0.0870 chunk 128 optimal weight: 0.8980 chunk 172 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN B 343 GLN C 343 GLN D 343 GLN E 343 GLN F 343 GLN G 343 GLN G 454 GLN H 343 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.158746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128255 restraints weight = 65879.402| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.07 r_work: 0.3306 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20704 Z= 0.118 Angle : 0.541 8.398 27952 Z= 0.280 Chirality : 0.041 0.147 3240 Planarity : 0.004 0.040 3592 Dihedral : 4.554 19.671 2896 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.72 % Favored : 95.97 % Rotamer: Outliers : 1.73 % Allowed : 19.38 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.17), residues: 2632 helix: 2.46 (0.16), residues: 1168 sheet: -0.66 (0.26), residues: 264 loop : -0.15 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 253 TYR 0.012 0.001 TYR H 353 PHE 0.006 0.001 PHE H 24 HIS 0.002 0.001 HIS F -20 Details of bonding type rmsd covalent geometry : bond 0.00272 (20704) covalent geometry : angle 0.54133 (27952) hydrogen bonds : bond 0.03819 ( 962) hydrogen bonds : angle 5.27722 ( 2745) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 544 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6530 (tpp) cc_final: 0.6078 (tpp) REVERT: A 60 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8795 (m) REVERT: A 62 LYS cc_start: 0.8678 (mttp) cc_final: 0.8261 (mmmt) REVERT: A 349 LYS cc_start: 0.8914 (mmtp) cc_final: 0.8640 (mmtt) REVERT: A 394 THR cc_start: 0.8989 (m) cc_final: 0.8753 (p) REVERT: A 454 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7628 (mm110) REVERT: B 60 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8717 (m) REVERT: B 62 LYS cc_start: 0.8703 (mmtp) cc_final: 0.8302 (mmmm) REVERT: B 66 ILE cc_start: 0.9131 (mt) cc_final: 0.8921 (mm) REVERT: B 94 ASN cc_start: 0.8256 (m110) cc_final: 0.7959 (t0) REVERT: B 242 LYS cc_start: 0.7839 (mttt) cc_final: 0.7567 (mmmt) REVERT: B 394 THR cc_start: 0.8890 (m) cc_final: 0.8483 (t) REVERT: C 60 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8740 (m) REVERT: C 62 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8338 (mmmm) REVERT: C 242 LYS cc_start: 0.7938 (mttt) cc_final: 0.7651 (mmmt) REVERT: C 500 GLU cc_start: 0.6779 (tt0) cc_final: 0.6469 (pt0) REVERT: D 21 GLN cc_start: 0.8581 (mt0) cc_final: 0.8376 (mt0) REVERT: D 60 THR cc_start: 0.9153 (t) cc_final: 0.8721 (m) REVERT: D 62 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8277 (mmmm) REVERT: D 85 MET cc_start: 0.8008 (mmm) cc_final: 0.7755 (mmm) REVERT: D 242 LYS cc_start: 0.7955 (mttt) cc_final: 0.7633 (mmmt) REVERT: D 454 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7726 (mm110) REVERT: D 500 GLU cc_start: 0.6630 (tt0) cc_final: 0.6378 (pt0) REVERT: E 60 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8713 (m) REVERT: E 62 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8318 (mmmm) REVERT: E 242 LYS cc_start: 0.7890 (mttt) cc_final: 0.7543 (mmmt) REVERT: E 277 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.6252 (tm-30) REVERT: E 394 THR cc_start: 0.9009 (m) cc_final: 0.8762 (p) REVERT: E 500 GLU cc_start: 0.6513 (tt0) cc_final: 0.6212 (pt0) REVERT: F 60 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8788 (m) REVERT: F 62 LYS cc_start: 0.8660 (mttt) cc_final: 0.8309 (mmmm) REVERT: F 78 MET cc_start: 0.8638 (tpp) cc_final: 0.8292 (tpp) REVERT: F 82 MET cc_start: 0.8269 (mmm) cc_final: 0.8035 (mmm) REVERT: F 98 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7547 (mm-30) REVERT: F 242 LYS cc_start: 0.7935 (mttt) cc_final: 0.7561 (mmmt) REVERT: F 337 MET cc_start: 0.5248 (pmm) cc_final: 0.4658 (pmt) REVERT: F 394 THR cc_start: 0.8974 (m) cc_final: 0.8719 (p) REVERT: G 60 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8765 (m) REVERT: G 62 LYS cc_start: 0.8672 (mmtp) cc_final: 0.8279 (mmmm) REVERT: G 78 MET cc_start: 0.8636 (tpp) cc_final: 0.8330 (tpp) REVERT: G 242 LYS cc_start: 0.7842 (mttt) cc_final: 0.7505 (mmmt) REVERT: G 335 GLU cc_start: 0.5571 (OUTLIER) cc_final: 0.5334 (mp0) REVERT: G 394 THR cc_start: 0.8957 (m) cc_final: 0.8732 (p) REVERT: H 1 MET cc_start: 0.6018 (tpp) cc_final: 0.4937 (tpp) REVERT: H 60 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8682 (m) REVERT: H 98 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7610 (mm-30) REVERT: H 349 LYS cc_start: 0.8912 (mmtp) cc_final: 0.8640 (mmtt) REVERT: H 454 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7636 (mm110) outliers start: 37 outliers final: 29 residues processed: 570 average time/residue: 1.3309 time to fit residues: 865.5915 Evaluate side-chains 566 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 528 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 161 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN B 343 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN D 241 GLN D 343 GLN E 343 GLN F 241 GLN F 343 GLN F 454 GLN G 343 GLN H 343 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.158120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126883 restraints weight = 65467.389| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.12 r_work: 0.3294 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20704 Z= 0.189 Angle : 0.574 9.716 27952 Z= 0.300 Chirality : 0.042 0.145 3240 Planarity : 0.004 0.039 3592 Dihedral : 4.657 19.557 2896 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.91 % Favored : 95.78 % Rotamer: Outliers : 1.87 % Allowed : 19.90 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.23 (0.17), residues: 2632 helix: 2.23 (0.16), residues: 1168 sheet: -0.66 (0.26), residues: 264 loop : -0.22 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 253 TYR 0.012 0.002 TYR F 353 PHE 0.012 0.001 PHE C 110 HIS 0.003 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00447 (20704) covalent geometry : angle 0.57386 (27952) hydrogen bonds : bond 0.04349 ( 962) hydrogen bonds : angle 5.37456 ( 2745) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 519 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6491 (tpp) cc_final: 0.6148 (tpp) REVERT: A 28 ASP cc_start: 0.7653 (p0) cc_final: 0.7215 (p0) REVERT: A 60 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8793 (m) REVERT: A 62 LYS cc_start: 0.8664 (mttp) cc_final: 0.8250 (mmmt) REVERT: A 349 LYS cc_start: 0.8968 (mmtp) cc_final: 0.8711 (mmtt) REVERT: A 394 THR cc_start: 0.8959 (m) cc_final: 0.8725 (p) REVERT: A 470 ASP cc_start: 0.8342 (m-30) cc_final: 0.8077 (m-30) REVERT: B 60 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8741 (m) REVERT: B 62 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8293 (mmmm) REVERT: B 66 ILE cc_start: 0.9150 (mt) cc_final: 0.8932 (mm) REVERT: B 94 ASN cc_start: 0.8310 (m110) cc_final: 0.8000 (t0) REVERT: B 242 LYS cc_start: 0.7897 (mttt) cc_final: 0.7647 (mmmt) REVERT: B 394 THR cc_start: 0.8912 (m) cc_final: 0.8519 (t) REVERT: C 60 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8764 (m) REVERT: C 62 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8346 (mmmm) REVERT: C 242 LYS cc_start: 0.7962 (mttt) cc_final: 0.7696 (mmmt) REVERT: C 389 LEU cc_start: 0.8156 (mt) cc_final: 0.7935 (mp) REVERT: C 500 GLU cc_start: 0.6843 (tt0) cc_final: 0.6522 (pt0) REVERT: D 21 GLN cc_start: 0.8585 (mt0) cc_final: 0.8369 (mt0) REVERT: D 60 THR cc_start: 0.9130 (t) cc_final: 0.8710 (m) REVERT: D 62 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8292 (mmmm) REVERT: D 85 MET cc_start: 0.8051 (mmm) cc_final: 0.7823 (mmm) REVERT: D 242 LYS cc_start: 0.7882 (mttt) cc_final: 0.7596 (mmmt) REVERT: D 454 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7655 (mm110) REVERT: D 500 GLU cc_start: 0.6789 (tt0) cc_final: 0.6519 (pt0) REVERT: E 60 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8743 (m) REVERT: E 62 LYS cc_start: 0.8667 (mmtm) cc_final: 0.8315 (mmmm) REVERT: E 242 LYS cc_start: 0.7928 (mttt) cc_final: 0.7599 (mmmt) REVERT: E 277 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.6155 (tm-30) REVERT: E 500 GLU cc_start: 0.6583 (tt0) cc_final: 0.6269 (pt0) REVERT: F 60 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8798 (m) REVERT: F 62 LYS cc_start: 0.8673 (mttt) cc_final: 0.8355 (mmmm) REVERT: F 82 MET cc_start: 0.8310 (mmm) cc_final: 0.8087 (mmm) REVERT: F 242 LYS cc_start: 0.7957 (mttt) cc_final: 0.7588 (mmmt) REVERT: F 337 MET cc_start: 0.5181 (pmm) cc_final: 0.4613 (pmt) REVERT: F 352 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8348 (tm-30) REVERT: F 394 THR cc_start: 0.8986 (m) cc_final: 0.8730 (p) REVERT: G 60 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8790 (m) REVERT: G 62 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8292 (mmmm) REVERT: G 78 MET cc_start: 0.8705 (tpp) cc_final: 0.8492 (tpp) REVERT: G 242 LYS cc_start: 0.7922 (mttt) cc_final: 0.7592 (mmmt) REVERT: G 335 GLU cc_start: 0.5559 (OUTLIER) cc_final: 0.5294 (mp0) REVERT: G 394 THR cc_start: 0.8982 (m) cc_final: 0.8755 (p) REVERT: H 60 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8673 (m) REVERT: H 98 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7648 (mm-30) REVERT: H 349 LYS cc_start: 0.8948 (mmtp) cc_final: 0.8681 (mmtt) REVERT: H 454 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7725 (mm110) outliers start: 40 outliers final: 29 residues processed: 548 average time/residue: 1.3125 time to fit residues: 818.9112 Evaluate side-chains 550 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 512 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -9 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue -9 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue -9 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue -9 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue -9 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain G residue -9 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 138 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 242 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN C 241 GLN C 343 GLN D 241 GLN E 343 GLN F 343 GLN F 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.159667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128622 restraints weight = 65833.640| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.12 r_work: 0.3310 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20704 Z= 0.132 Angle : 0.541 8.597 27952 Z= 0.282 Chirality : 0.041 0.143 3240 Planarity : 0.004 0.046 3592 Dihedral : 4.540 19.407 2896 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.69 % Favored : 96.01 % Rotamer: Outliers : 1.78 % Allowed : 20.13 % Favored : 78.09 % 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: 1.46 (0.17), residues: 2632 helix: 2.44 (0.16), residues: 1168 sheet: -0.50 (0.26), residues: 264 loop : -0.13 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 253 TYR 0.011 0.001 TYR G 353 PHE 0.007 0.001 PHE H 44 HIS 0.003 0.001 HIS F 296 Details of bonding type rmsd covalent geometry : bond 0.00309 (20704) covalent geometry : angle 0.54082 (27952) hydrogen bonds : bond 0.03903 ( 962) hydrogen bonds : angle 5.27300 ( 2745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17725.01 seconds wall clock time: 299 minutes 33.65 seconds (17973.65 seconds total)