Starting phenix.real_space_refine on Mon Oct 26 04:42:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11lp_75811/10_2026/11lp_75811.cif Found real_map, /net/cci-nas-00/data/ceres_data/11lp_75811/10_2026/11lp_75811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11lp_75811/10_2026/11lp_75811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11lp_75811/10_2026/11lp_75811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11lp_75811/10_2026/11lp_75811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11lp_75811/10_2026/11lp_75811.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12144 2.51 5 N 3228 2.21 5 O 3684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19176 Number of models: 1 Model: "" Number of chains: 18 Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 816 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "G" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "B" Number of atoms: 2831 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 363, 2831 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 23, 'TRANS': 339} Chain breaks: 3 Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 816 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 816 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 2831 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 363, 2831 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 23, 'TRANS': 339} Chain breaks: 3 Chain: "A" Number of atoms: 2831 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 363, 2831 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 23, 'TRANS': 339} Chain breaks: 3 Chain: "I" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "E" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "O" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 814 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "J" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 814 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "N" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 814 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.94, per 1000 atoms: 0.21 Number of scatterers: 19176 At special positions: 0 Unit cell: (148.685, 158.822, 118.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3684 8.00 N 3228 7.00 C 12144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 283 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG ACYS B 61 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG ACYS C 61 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 228 " distance=2.03 Simple disulfide: pdb=" SG CYS C 223 " - pdb=" SG CYS C 252 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG ACYS A 61 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 158 " " NAG A 502 " - " ASN A 247 " " NAG A 503 " - " ASN A 319 " " NAG B 501 " - " ASN B 158 " " NAG B 502 " - " ASN B 247 " " NAG B 503 " - " ASN B 319 " " NAG C 501 " - " ASN C 158 " " NAG C 502 " - " ASN C 247 " " NAG C 503 " - " ASN C 319 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 775.2 milliseconds 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4470 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 54 sheets defined 12.4% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'M' and resid 88 through 92 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.667A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 90 through 104 Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.782A pdb=" N GLU B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.948A pdb=" N ASN B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 294 Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 334 through 339 removed outlier: 4.244A pdb=" N ILE B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'B' and resid 385 through 388 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 106 through 113 removed outlier: 3.793A pdb=" N GLU C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.940A pdb=" N ASN C 158 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 294 Processing helix chain 'C' and resid 298 through 304 removed outlier: 3.507A pdb=" N LEU C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 339 removed outlier: 4.263A pdb=" N ILE C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 380 Processing helix chain 'C' and resid 385 through 388 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.792A pdb=" N GLU A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.923A pdb=" N ASN A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 294 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.521A pdb=" N LEU A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.265A pdb=" N ILE A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 385 through 388 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.668A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.671A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'O' and resid 88 through 92 Processing helix chain 'L' and resid 29 through 33 removed outlier: 3.982A pdb=" N ASN L 32 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE L 33 " --> pdb=" O GLY L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 33' Processing helix chain 'L' and resid 79 through 84 removed outlier: 3.560A pdb=" N ALA L 84 " --> pdb=" O GLU L 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 removed outlier: 3.998A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE J 33 " --> pdb=" O GLY J 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 29 through 33' Processing helix chain 'J' and resid 79 through 84 removed outlier: 3.563A pdb=" N ALA J 84 " --> pdb=" O GLU J 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 33 removed outlier: 3.980A pdb=" N ASN N 32 " --> pdb=" O VAL N 29 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE N 33 " --> pdb=" O GLY N 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 29 through 33' Processing helix chain 'N' and resid 79 through 84 removed outlier: 3.554A pdb=" N ALA N 84 " --> pdb=" O GLU N 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AA3, first strand: chain 'F' and resid 46 through 49 removed outlier: 5.569A pdb=" N LEU F 47 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.689A pdb=" N THR M 79 " --> pdb=" O ASP M 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.567A pdb=" N GLY M 50 " --> pdb=" O TRP M 37 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS M 39 " --> pdb=" O TRP M 48 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TRP M 48 " --> pdb=" O LYS M 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.562A pdb=" N TYR M 110 " --> pdb=" O ARG M 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 8 Processing sheet with id=AA8, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.815A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG G 39 " --> pdb=" O TRP G 48 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.463A pdb=" N TYR B 5 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS B 328 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU B 11 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP B 326 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.463A pdb=" N TYR B 5 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS B 328 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU B 11 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP B 326 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 216 through 218 removed outlier: 4.786A pdb=" N THR B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS B 202 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET B 44 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 46 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TRP B 240 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 87 removed outlier: 4.735A pdb=" N ILE B 54 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.742A pdb=" N VAL B 133 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 135 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B 60 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AB6, first strand: chain 'B' and resid 346 through 347 Processing sheet with id=AB7, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AB9, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AC1, first strand: chain 'D' and resid 46 through 49 removed outlier: 5.562A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AC4, first strand: chain 'H' and resid 46 through 49 removed outlier: 5.574A pdb=" N LEU H 47 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.437A pdb=" N TYR C 5 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS C 328 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU C 11 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP C 326 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.437A pdb=" N TYR C 5 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS C 328 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU C 11 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP C 326 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 316 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 216 through 218 removed outlier: 4.777A pdb=" N THR C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS C 202 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET C 44 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C 46 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TRP C 240 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 223 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 87 removed outlier: 4.723A pdb=" N ILE C 54 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 131 through 135 removed outlier: 3.797A pdb=" N VAL C 133 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 62 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 135 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C 60 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AD2, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AD3, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AD4, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.446A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.446A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 316 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 216 through 218 removed outlier: 4.783A pdb=" N THR A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS A 202 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET A 44 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 46 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TRP A 240 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS A 223 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.515A pdb=" N LYS A 85 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE A 54 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 131 through 135 removed outlier: 3.784A pdb=" N VAL A 133 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 62 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 135 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 60 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AE1, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AE2, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AE3, first strand: chain 'I' and resid 5 through 8 Processing sheet with id=AE4, first strand: chain 'I' and resid 12 through 13 removed outlier: 3.832A pdb=" N GLY I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG I 39 " --> pdb=" O TRP I 48 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TRP I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AE6, first strand: chain 'E' and resid 12 through 13 removed outlier: 3.823A pdb=" N GLY E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG E 39 " --> pdb=" O TRP E 48 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.693A pdb=" N THR K 79 " --> pdb=" O ASP K 74 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.570A pdb=" N GLY K 50 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS K 39 " --> pdb=" O TRP K 48 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TRP K 48 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.572A pdb=" N TYR K 110 " --> pdb=" O ARG K 99 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.685A pdb=" N THR O 79 " --> pdb=" O ASP O 74 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.889A pdb=" N GLU O 11 " --> pdb=" O THR O 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'O' and resid 59 through 61 removed outlier: 5.433A pdb=" N TRP O 48 " --> pdb=" O LYS O 39 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS O 39 " --> pdb=" O TRP O 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR O 110 " --> pdb=" O ARG O 99 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AF5, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.703A pdb=" N SER L 50 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AF7, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.694A pdb=" N SER J 50 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU J 47 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AF9, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.701A pdb=" N SER N 50 " --> pdb=" O TYR N 53 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU N 47 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6066 1.34 - 1.46: 5018 1.46 - 1.58: 8386 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 19644 Sorted by residual: bond pdb=" N GLU M 2 " pdb=" CA GLU M 2 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N GLU O 2 " pdb=" CA GLU O 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N GLU K 2 " pdb=" CA GLU K 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N LYS C 1 " pdb=" CA LYS C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N LYS A 1 " pdb=" CA LYS A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 ... (remaining 19639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 26395 1.99 - 3.97: 228 3.97 - 5.96: 23 5.96 - 7.94: 0 7.94 - 9.93: 6 Bond angle restraints: 26652 Sorted by residual: angle pdb=" CB LEU C 322 " pdb=" CG LEU C 322 " pdb=" CD2 LEU C 322 " ideal model delta sigma weight residual 110.70 120.63 -9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CB LEU A 322 " pdb=" CG LEU A 322 " pdb=" CD2 LEU A 322 " ideal model delta sigma weight residual 110.70 120.55 -9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CB LEU B 322 " pdb=" CG LEU B 322 " pdb=" CD2 LEU B 322 " ideal model delta sigma weight residual 110.70 120.52 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CB LEU B 322 " pdb=" CG LEU B 322 " pdb=" CD1 LEU B 322 " ideal model delta sigma weight residual 110.70 120.51 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CB LEU A 322 " pdb=" CG LEU A 322 " pdb=" CD1 LEU A 322 " ideal model delta sigma weight residual 110.70 120.47 -9.77 3.00e+00 1.11e-01 1.06e+01 ... (remaining 26647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 10756 16.54 - 33.08: 777 33.08 - 49.61: 162 49.61 - 66.15: 65 66.15 - 82.69: 12 Dihedral angle restraints: 11772 sinusoidal: 4734 harmonic: 7038 Sorted by residual: dihedral pdb=" CD ARG C 333 " pdb=" NE ARG C 333 " pdb=" CZ ARG C 333 " pdb=" NH1 ARG C 333 " ideal model delta sinusoidal sigma weight residual 0.00 59.22 -59.22 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CD ARG A 333 " pdb=" NE ARG A 333 " pdb=" CZ ARG A 333 " pdb=" NH1 ARG A 333 " ideal model delta sinusoidal sigma weight residual 0.00 59.12 -59.12 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS C 159 " pdb=" SG CYS C 159 " pdb=" SG CYS C 169 " pdb=" CB CYS C 169 " ideal model delta sinusoidal sigma weight residual 93.00 138.66 -45.66 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 11769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 2940 0.329 - 0.658: 0 0.658 - 0.987: 0 0.987 - 1.316: 0 1.316 - 1.645: 3 Chirality restraints: 2943 Sorted by residual: chirality pdb=" CG LEU B 322 " pdb=" CB LEU B 322 " pdb=" CD1 LEU B 322 " pdb=" CD2 LEU B 322 " both_signs ideal model delta sigma weight residual False -2.59 -0.94 -1.64 2.00e-01 2.50e+01 6.76e+01 chirality pdb=" CG LEU A 322 " pdb=" CB LEU A 322 " pdb=" CD1 LEU A 322 " pdb=" CD2 LEU A 322 " both_signs ideal model delta sigma weight residual False -2.59 -0.96 -1.63 2.00e-01 2.50e+01 6.68e+01 chirality pdb=" CG LEU C 322 " pdb=" CB LEU C 322 " pdb=" CD1 LEU C 322 " pdb=" CD2 LEU C 322 " both_signs ideal model delta sigma weight residual False -2.59 -0.97 -1.62 2.00e-01 2.50e+01 6.55e+01 ... (remaining 2940 not shown) Planarity restraints: 3366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 333 " -0.770 9.50e-02 1.11e+02 3.47e-01 8.58e+01 pdb=" NE ARG C 333 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG C 333 " -0.054 2.00e-02 2.50e+03 pdb=" NH1 ARG C 333 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG C 333 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 333 " -0.768 9.50e-02 1.11e+02 3.46e-01 8.55e+01 pdb=" NE ARG A 333 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG A 333 " -0.054 2.00e-02 2.50e+03 pdb=" NH1 ARG A 333 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 333 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 40 " 0.403 9.50e-02 1.11e+02 1.82e-01 2.46e+01 pdb=" NE ARG N 40 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG N 40 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG N 40 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG N 40 " 0.002 2.00e-02 2.50e+03 ... (remaining 3363 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 276 2.66 - 3.22: 18507 3.22 - 3.78: 28526 3.78 - 4.34: 40734 4.34 - 4.90: 66558 Nonbonded interactions: 154601 Sorted by model distance: nonbonded pdb=" OE2 GLU C 31 " pdb=" OH TYR I 109 " model vdw 2.097 3.040 nonbonded pdb=" OH TYR G 109 " pdb=" OE2 GLU B 31 " model vdw 2.125 3.040 nonbonded pdb=" OE2 GLU A 31 " pdb=" OH TYR E 109 " model vdw 2.129 3.040 nonbonded pdb=" O SER K 8 " pdb=" OG1 THR K 115 " model vdw 2.212 3.040 nonbonded pdb=" O SER M 8 " pdb=" OG1 THR M 115 " model vdw 2.216 3.040 ... (remaining 154596 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: 0.03 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'A' } ncs_group { reference = chain 'L' selection = chain 'J' selection = chain 'N' } 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.820 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.003 0.034 19686 Z= 0.125 Angle : 0.511 9.931 26745 Z= 0.257 Chirality : 0.067 1.645 2943 Planarity : 0.014 0.347 3357 Dihedral : 12.376 82.690 7203 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.00 (0.17), residues: 2403 helix: 1.61 (0.37), residues: 198 sheet: 0.77 (0.20), residues: 738 loop : 0.60 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.004 ARG A 333 TYR 0.020 0.001 TYR L 91 PHE 0.009 0.001 PHE I 79 TRP 0.011 0.001 TRP N 35 HIS 0.003 0.001 HIS N 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (19644) covalent geometry : angle 0.50962 / 0.26 (26652) SS BOND : bond 0.00171 / 0.11 ( 33) SS BOND : angle 0.66276 / 0.45 ( 66) hydrogen bonds : bond 0.25177 / 16.60 ( 632) hydrogen bonds : angle 9.63216 / 6.69 ( 1596) link_NAG-ASN : bond 0.00046 / 0.03 ( 9) link_NAG-ASN : angle 1.02445 / 0.66 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7660 (t0) cc_final: 0.7301 (t70) REVERT: F 13 THR cc_start: 0.9687 (m) cc_final: 0.9242 (t) REVERT: F 37 TYR cc_start: 0.9409 (m-80) cc_final: 0.9177 (m-80) REVERT: F 108 THR cc_start: 0.8459 (m) cc_final: 0.8232 (p) REVERT: M 71 MET cc_start: 0.8924 (mmt) cc_final: 0.8643 (mmm) REVERT: M 91 ASP cc_start: 0.9020 (m-30) cc_final: 0.8648 (m-30) REVERT: D 12 ASP cc_start: 0.7930 (t0) cc_final: 0.7543 (t70) REVERT: D 13 THR cc_start: 0.9651 (m) cc_final: 0.9007 (t) REVERT: D 54 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8267 (mmmm) REVERT: D 100 LEU cc_start: 0.9234 (mt) cc_final: 0.9011 (mp) REVERT: H 12 ASP cc_start: 0.7635 (t0) cc_final: 0.6970 (t0) REVERT: H 13 THR cc_start: 0.9631 (m) cc_final: 0.9044 (t) REVERT: H 16 GLN cc_start: 0.8640 (mp10) cc_final: 0.8358 (mp10) REVERT: H 28 ASN cc_start: 0.8755 (p0) cc_final: 0.8521 (p0) REVERT: H 46 LYS cc_start: 0.9115 (ptmm) cc_final: 0.8842 (ptmm) REVERT: H 54 LYS cc_start: 0.8761 (mmtp) cc_final: 0.8557 (mmmm) REVERT: K 64 LYS cc_start: 0.9284 (ttpt) cc_final: 0.8813 (ttpp) REVERT: K 71 MET cc_start: 0.9016 (mmt) cc_final: 0.8644 (mmt) REVERT: K 116 LEU cc_start: 0.9438 (tp) cc_final: 0.9196 (tt) REVERT: O 71 MET cc_start: 0.8976 (mmt) cc_final: 0.8662 (mmm) REVERT: O 116 LEU cc_start: 0.9573 (tp) cc_final: 0.9336 (tt) REVERT: L 49 TYR cc_start: 0.7428 (p90) cc_final: 0.7204 (p90) REVERT: L 77 ASN cc_start: 0.8241 (t0) cc_final: 0.8038 (t0) REVERT: L 82 ASP cc_start: 0.8843 (m-30) cc_final: 0.8552 (m-30) REVERT: L 103 LYS cc_start: 0.8781 (tppp) cc_final: 0.8273 (tppt) REVERT: J 49 TYR cc_start: 0.7527 (p90) cc_final: 0.7248 (p90) REVERT: J 82 ASP cc_start: 0.8720 (m-30) cc_final: 0.8173 (m-30) REVERT: J 103 LYS cc_start: 0.8696 (tppp) cc_final: 0.8237 (tptt) REVERT: N 79 GLN cc_start: 0.7253 (mt0) cc_final: 0.6921 (tm-30) REVERT: N 81 GLU cc_start: 0.8559 (pt0) cc_final: 0.8300 (pm20) REVERT: N 82 ASP cc_start: 0.8755 (m-30) cc_final: 0.8553 (m-30) REVERT: N 103 LYS cc_start: 0.8833 (tppp) cc_final: 0.8520 (tppt) outliers start: 0 outliers final: 1 residues processed: 406 average time/residue: 0.6646 time to fit residues: 300.2270 Evaluate side-chains 296 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 12 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.0000 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 39 GLN G 40 GLN B 397 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN C 397 HIS A 397 HIS I 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN L 8 GLN L 28 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.049014 restraints weight = 56523.683| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.71 r_work: 0.2658 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19686 Z= 0.237 Angle : 0.697 9.447 26745 Z= 0.362 Chirality : 0.047 0.167 2943 Planarity : 0.005 0.055 3357 Dihedral : 5.247 35.272 2861 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.13 % Allowed : 11.33 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2403 helix: 1.49 (0.35), residues: 198 sheet: 0.59 (0.18), residues: 804 loop : 0.43 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 17 TYR 0.029 0.002 TYR C 175 PHE 0.019 0.002 PHE I 79 TRP 0.011 0.001 TRP K 111 HIS 0.009 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (19644) covalent geometry : angle 0.69467 / 0.36 (26652) SS BOND : bond 0.00532 / 0.37 ( 33) SS BOND : angle 1.16326 / 0.77 ( 66) hydrogen bonds : bond 0.04154 / 2.81 ( 632) hydrogen bonds : angle 6.26944 / 4.37 ( 1596) link_NAG-ASN : bond 0.00133 / 0.09 ( 9) link_NAG-ASN : angle 1.21611 / 0.76 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 326 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.8669 (t0) cc_final: 0.8129 (t70) REVERT: F 13 THR cc_start: 0.9730 (m) cc_final: 0.9326 (p) REVERT: F 16 GLN cc_start: 0.8685 (mp10) cc_final: 0.8299 (mp10) REVERT: F 35 TYR cc_start: 0.9074 (m-80) cc_final: 0.8857 (m-80) REVERT: F 37 TYR cc_start: 0.9523 (m-80) cc_final: 0.9216 (m-80) REVERT: F 79 LEU cc_start: 0.8625 (mp) cc_final: 0.8394 (mp) REVERT: F 100 LEU cc_start: 0.9241 (mt) cc_final: 0.8988 (mt) REVERT: M 14 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7228 (tpm170) REVERT: M 24 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8319 (ttmm) REVERT: M 45 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.8176 (ptp90) REVERT: M 47 GLU cc_start: 0.8356 (pm20) cc_final: 0.8136 (pm20) REVERT: M 86 ARG cc_start: 0.9243 (mmp80) cc_final: 0.8935 (mmp80) REVERT: M 87 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.7719 (mm) REVERT: M 90 GLU cc_start: 0.9126 (pm20) cc_final: 0.8889 (pm20) REVERT: M 91 ASP cc_start: 0.9110 (m-30) cc_final: 0.8596 (m-30) REVERT: B 102 MET cc_start: 0.8494 (mmp) cc_final: 0.8243 (mmm) REVERT: B 187 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7158 (ptt) REVERT: D 12 ASP cc_start: 0.8755 (t0) cc_final: 0.7925 (t0) REVERT: D 16 GLN cc_start: 0.8713 (mp10) cc_final: 0.8313 (pm20) REVERT: D 29 ILE cc_start: 0.8266 (mm) cc_final: 0.8049 (mt) REVERT: D 35 TYR cc_start: 0.9147 (m-80) cc_final: 0.8717 (m-80) REVERT: H 12 ASP cc_start: 0.8472 (t0) cc_final: 0.8057 (t0) REVERT: H 13 THR cc_start: 0.9679 (m) cc_final: 0.9250 (t) REVERT: H 16 GLN cc_start: 0.8857 (mp10) cc_final: 0.8573 (mp10) REVERT: H 43 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8733 (p) REVERT: H 46 LYS cc_start: 0.9064 (ptmm) cc_final: 0.8683 (ptmm) REVERT: H 48 LEU cc_start: 0.9459 (tm) cc_final: 0.9231 (tt) REVERT: H 53 ASP cc_start: 0.8484 (p0) cc_final: 0.8243 (p0) REVERT: H 54 LYS cc_start: 0.8962 (mmtp) cc_final: 0.8437 (mmmm) REVERT: C 102 MET cc_start: 0.8495 (mmm) cc_final: 0.8268 (mmm) REVERT: C 175 TYR cc_start: 0.9034 (m-80) cc_final: 0.8829 (m-80) REVERT: A 56 MET cc_start: 0.8097 (tpp) cc_final: 0.7475 (mtp) REVERT: A 175 TYR cc_start: 0.9248 (m-10) cc_final: 0.9042 (m-10) REVERT: A 368 ASP cc_start: 0.9376 (m-30) cc_final: 0.9120 (p0) REVERT: I 2 GLN cc_start: 0.8995 (tp40) cc_final: 0.8131 (tp-100) REVERT: I 28 ASP cc_start: 0.8526 (t0) cc_final: 0.8311 (t0) REVERT: I 76 LYS cc_start: 0.9565 (mtpm) cc_final: 0.9347 (mtmm) REVERT: E 39 ARG cc_start: 0.9082 (ttp-170) cc_final: 0.8833 (ttp80) REVERT: E 84 ASN cc_start: 0.9289 (t0) cc_final: 0.8970 (m110) REVERT: E 102 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8482 (m-30) REVERT: K 24 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8027 (tttp) REVERT: K 64 LYS cc_start: 0.9471 (ttpt) cc_final: 0.8936 (ttpp) REVERT: K 86 ARG cc_start: 0.9000 (mmp80) cc_final: 0.8739 (mmp80) REVERT: O 45 ARG cc_start: 0.7685 (tpp80) cc_final: 0.7348 (tpp80) REVERT: O 66 LYS cc_start: 0.9190 (ttmm) cc_final: 0.8617 (mmmt) REVERT: O 86 ARG cc_start: 0.9011 (mmp80) cc_final: 0.8678 (mmp80) REVERT: O 113 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8343 (pm20) REVERT: L 11 MET cc_start: 0.8340 (mtp) cc_final: 0.7880 (mtp) REVERT: L 49 TYR cc_start: 0.8273 (p90) cc_final: 0.7905 (p90) REVERT: L 77 ASN cc_start: 0.8776 (t0) cc_final: 0.8497 (t0) REVERT: L 85 GLU cc_start: 0.7583 (tp30) cc_final: 0.7082 (tp30) REVERT: J 49 TYR cc_start: 0.8369 (p90) cc_final: 0.8006 (p90) REVERT: J 77 ASN cc_start: 0.8502 (t0) cc_final: 0.8254 (t0) REVERT: J 103 LYS cc_start: 0.8678 (tppp) cc_final: 0.7773 (tppt) REVERT: N 11 MET cc_start: 0.8356 (mtp) cc_final: 0.8115 (mtp) REVERT: N 27 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8244 (tm-30) REVERT: N 77 ASN cc_start: 0.8701 (t0) cc_final: 0.7976 (t0) REVERT: N 79 GLN cc_start: 0.7475 (mt0) cc_final: 0.7103 (mp10) REVERT: N 81 GLU cc_start: 0.8633 (pt0) cc_final: 0.8286 (pm20) REVERT: N 82 ASP cc_start: 0.8615 (m-30) cc_final: 0.7848 (m-30) REVERT: N 103 LYS cc_start: 0.8629 (tppp) cc_final: 0.8264 (tppt) outliers start: 45 outliers final: 15 residues processed: 348 average time/residue: 0.6597 time to fit residues: 255.4096 Evaluate side-chains 306 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 283 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain M residue 14 ARG Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 24 LYS Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 113 GLN Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain N residue 94 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: [194, 205, 67, 21, 213, 227, 73, 134, 231, 106, 192] chunk 194 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 HIS ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN O 7 GLN O 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.046130 restraints weight = 57299.302| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.68 r_work: 0.2580 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 19686 Z= 0.365 Angle : 0.735 8.774 26745 Z= 0.382 Chirality : 0.048 0.191 2943 Planarity : 0.005 0.064 3357 Dihedral : 5.369 32.789 2859 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.75 % Allowed : 14.41 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2403 helix: 0.60 (0.33), residues: 216 sheet: 0.29 (0.17), residues: 831 loop : 0.14 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 39 TYR 0.037 0.002 TYR J 49 PHE 0.023 0.002 PHE I 79 TRP 0.010 0.001 TRP O 111 HIS 0.005 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.37 (19644) covalent geometry : angle 0.73131 / 0.38 (26652) SS BOND : bond 0.00397 / 0.27 ( 33) SS BOND : angle 1.35464 / 0.94 ( 66) hydrogen bonds : bond 0.04404 / 2.97 ( 632) hydrogen bonds : angle 5.99974 / 4.20 ( 1596) link_NAG-ASN : bond 0.00210 / 0.13 ( 9) link_NAG-ASN : angle 1.41325 / 0.89 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.8853 (t0) cc_final: 0.8568 (t70) REVERT: F 13 THR cc_start: 0.9752 (m) cc_final: 0.9427 (t) REVERT: F 17 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7623 (tpp80) REVERT: F 37 TYR cc_start: 0.9534 (m-80) cc_final: 0.9214 (m-80) REVERT: F 62 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7966 (ptp90) REVERT: F 83 ASP cc_start: 0.7327 (m-30) cc_final: 0.6982 (m-30) REVERT: M 14 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7343 (tpm170) REVERT: M 24 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8091 (ttpp) REVERT: M 39 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.7977 (tttp) REVERT: M 45 ARG cc_start: 0.8692 (ttp-110) cc_final: 0.8166 (ptp90) REVERT: M 47 GLU cc_start: 0.8436 (pm20) cc_final: 0.8165 (pm20) REVERT: M 87 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8486 (mm) REVERT: G 73 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7015 (p0) REVERT: G 76 LYS cc_start: 0.9517 (mtpm) cc_final: 0.9133 (mtmm) REVERT: B 102 MET cc_start: 0.8671 (mmp) cc_final: 0.8395 (mmm) REVERT: D 12 ASP cc_start: 0.8806 (t0) cc_final: 0.8060 (t0) REVERT: D 16 GLN cc_start: 0.8650 (mp10) cc_final: 0.8257 (pm20) REVERT: D 100 LEU cc_start: 0.8889 (mp) cc_final: 0.8648 (mt) REVERT: H 12 ASP cc_start: 0.8654 (t0) cc_final: 0.8151 (t0) REVERT: H 13 THR cc_start: 0.9731 (m) cc_final: 0.9271 (t) REVERT: H 16 GLN cc_start: 0.8949 (mp10) cc_final: 0.8545 (mp10) REVERT: H 43 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8834 (p) REVERT: H 54 LYS cc_start: 0.9198 (mmtp) cc_final: 0.8795 (mmmm) REVERT: C 102 MET cc_start: 0.8658 (mmm) cc_final: 0.8275 (mmm) REVERT: A 368 ASP cc_start: 0.9372 (m-30) cc_final: 0.9137 (p0) REVERT: I 2 GLN cc_start: 0.9016 (tp40) cc_final: 0.8171 (tp-100) REVERT: I 28 ASP cc_start: 0.8616 (t0) cc_final: 0.8390 (t0) REVERT: I 76 LYS cc_start: 0.9611 (mtpm) cc_final: 0.9387 (mtmm) REVERT: E 39 ARG cc_start: 0.9114 (ttp-170) cc_final: 0.8897 (ttp80) REVERT: E 102 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8590 (m-30) REVERT: K 64 LYS cc_start: 0.9388 (ttpt) cc_final: 0.8932 (ttpt) REVERT: K 86 ARG cc_start: 0.9115 (mmp80) cc_final: 0.8776 (mmp80) REVERT: O 24 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7899 (ttmm) REVERT: O 39 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8394 (tptm) REVERT: O 45 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7432 (tpp80) REVERT: O 113 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8877 (pm20) REVERT: O 116 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8926 (tm) REVERT: L 24 LYS cc_start: 0.9330 (ttmm) cc_final: 0.8830 (tppp) REVERT: L 40 ARG cc_start: 0.8624 (tmm-80) cc_final: 0.8376 (tmm-80) REVERT: L 85 GLU cc_start: 0.7820 (tp30) cc_final: 0.7423 (tp30) REVERT: J 11 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7960 (mtt) REVERT: J 81 GLU cc_start: 0.7883 (pm20) cc_final: 0.7521 (pm20) REVERT: J 82 ASP cc_start: 0.8983 (m-30) cc_final: 0.8664 (m-30) REVERT: J 85 GLU cc_start: 0.7844 (mp0) cc_final: 0.7583 (mp0) REVERT: J 103 LYS cc_start: 0.8532 (tppp) cc_final: 0.7991 (tppt) REVERT: N 27 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8109 (tm-30) REVERT: N 77 ASN cc_start: 0.8810 (t0) cc_final: 0.8186 (t0) REVERT: N 79 GLN cc_start: 0.7609 (mt0) cc_final: 0.7350 (mp10) REVERT: N 81 GLU cc_start: 0.8704 (pt0) cc_final: 0.8375 (pm20) REVERT: N 82 ASP cc_start: 0.8772 (m-30) cc_final: 0.7948 (m-30) REVERT: N 85 GLU cc_start: 0.7808 (tp30) cc_final: 0.7521 (tp30) REVERT: N 103 LYS cc_start: 0.8712 (tppp) cc_final: 0.8384 (tppt) outliers start: 58 outliers final: 19 residues processed: 324 average time/residue: 0.6617 time to fit residues: 238.7790 Evaluate side-chains 309 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 ARG Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 113 GLN Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: [223, 139, 119, 201, 7, 166, 233, 27, 224, 210, 14] chunk 223 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 201 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN O 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.047245 restraints weight = 56486.458| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.69 r_work: 0.2608 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19686 Z= 0.208 Angle : 0.660 9.654 26745 Z= 0.337 Chirality : 0.045 0.172 2943 Planarity : 0.004 0.057 3357 Dihedral : 4.953 29.085 2859 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.51 % Allowed : 16.22 % Favored : 81.27 % 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: 0.23 (0.17), residues: 2403 helix: 0.92 (0.35), residues: 198 sheet: 0.47 (0.17), residues: 781 loop : -0.07 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 45 TYR 0.024 0.002 TYR L 49 PHE 0.014 0.002 PHE I 79 TRP 0.008 0.001 TRP A 240 HIS 0.004 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (19644) covalent geometry : angle 0.65768 / 0.34 (26652) SS BOND : bond 0.00300 / 0.21 ( 33) SS BOND : angle 1.03465 / 0.70 ( 66) hydrogen bonds : bond 0.03683 / 2.49 ( 632) hydrogen bonds : angle 5.68876 / 3.99 ( 1596) link_NAG-ASN : bond 0.00084 / 0.06 ( 9) link_NAG-ASN : angle 1.21666 / 0.76 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.9003 (t0) cc_final: 0.8474 (t70) REVERT: F 13 THR cc_start: 0.9743 (m) cc_final: 0.9381 (t) REVERT: F 16 GLN cc_start: 0.9155 (mp10) cc_final: 0.8860 (mp10) REVERT: M 4 GLN cc_start: 0.6837 (pm20) cc_final: 0.6501 (pm20) REVERT: M 14 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7387 (tpm170) REVERT: M 24 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8156 (ttpp) REVERT: M 47 GLU cc_start: 0.8468 (pm20) cc_final: 0.8131 (pm20) REVERT: M 84 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8409 (mm) REVERT: M 87 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8627 (mm) REVERT: G 39 ARG cc_start: 0.9195 (ttp80) cc_final: 0.8988 (ttm-80) REVERT: B 102 MET cc_start: 0.8733 (mmp) cc_final: 0.8221 (mmm) REVERT: D 12 ASP cc_start: 0.8745 (t0) cc_final: 0.7907 (t0) REVERT: D 16 GLN cc_start: 0.8643 (mp10) cc_final: 0.8314 (pm20) REVERT: D 17 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8187 (ptm-80) REVERT: D 83 ASP cc_start: 0.7711 (m-30) cc_final: 0.6970 (m-30) REVERT: H 12 ASP cc_start: 0.8644 (t0) cc_final: 0.8427 (t70) REVERT: H 13 THR cc_start: 0.9722 (m) cc_final: 0.9430 (t) REVERT: H 17 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8538 (ttp80) REVERT: H 54 LYS cc_start: 0.9189 (mmtp) cc_final: 0.8650 (mmmm) REVERT: H 62 ARG cc_start: 0.9158 (ptp90) cc_final: 0.8910 (ptp90) REVERT: H 84 GLU cc_start: 0.9031 (pp20) cc_final: 0.8427 (pm20) REVERT: C 102 MET cc_start: 0.8692 (mmm) cc_final: 0.8258 (mmm) REVERT: A 56 MET cc_start: 0.8418 (tpp) cc_final: 0.8003 (mtp) REVERT: A 175 TYR cc_start: 0.9255 (m-10) cc_final: 0.9035 (m-10) REVERT: A 281 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8637 (mm-30) REVERT: A 368 ASP cc_start: 0.9377 (m-30) cc_final: 0.9163 (p0) REVERT: I 2 GLN cc_start: 0.8983 (tp40) cc_final: 0.8139 (tp-100) REVERT: I 28 ASP cc_start: 0.8643 (t0) cc_final: 0.8385 (t0) REVERT: I 76 LYS cc_start: 0.9612 (mtpm) cc_final: 0.9342 (mtmm) REVERT: E 76 LYS cc_start: 0.9673 (mtpp) cc_final: 0.9428 (mtmm) REVERT: E 84 ASN cc_start: 0.9317 (t0) cc_final: 0.9076 (m110) REVERT: K 12 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8749 (tm) REVERT: K 14 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7150 (tpm170) REVERT: K 47 GLU cc_start: 0.8106 (pm20) cc_final: 0.7856 (pm20) REVERT: K 64 LYS cc_start: 0.9370 (ttpt) cc_final: 0.9070 (ttpt) REVERT: K 86 ARG cc_start: 0.9148 (mmp80) cc_final: 0.8867 (mmp80) REVERT: O 4 GLN cc_start: 0.7613 (pp30) cc_final: 0.7244 (pp30) REVERT: O 24 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7658 (ttmm) REVERT: O 39 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8421 (tttp) REVERT: O 45 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7589 (tpp80) REVERT: O 66 LYS cc_start: 0.9140 (tppt) cc_final: 0.8493 (mmmt) REVERT: O 113 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.9096 (pm20) REVERT: O 116 LEU cc_start: 0.9211 (tt) cc_final: 0.8811 (tm) REVERT: L 24 LYS cc_start: 0.9341 (ttmm) cc_final: 0.9072 (tppp) REVERT: L 27 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7882 (tm-30) REVERT: L 40 ARG cc_start: 0.8668 (tmm-80) cc_final: 0.8468 (tmm-80) REVERT: L 49 TYR cc_start: 0.8354 (p90) cc_final: 0.8102 (p90) REVERT: L 85 GLU cc_start: 0.7851 (tp30) cc_final: 0.7434 (tp30) REVERT: J 8 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7855 (tp-100) REVERT: J 11 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7938 (mtt) REVERT: J 24 LYS cc_start: 0.8766 (mppt) cc_final: 0.8463 (mppt) REVERT: J 49 TYR cc_start: 0.8551 (p90) cc_final: 0.8286 (p90) REVERT: J 82 ASP cc_start: 0.8885 (m-30) cc_final: 0.8553 (m-30) REVERT: J 85 GLU cc_start: 0.7865 (mp0) cc_final: 0.7647 (mp0) REVERT: J 103 LYS cc_start: 0.8469 (tppp) cc_final: 0.8153 (tppt) REVERT: N 11 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8042 (mtt) REVERT: N 27 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8157 (tm-30) REVERT: N 77 ASN cc_start: 0.8828 (t0) cc_final: 0.8156 (t0) REVERT: N 81 GLU cc_start: 0.8699 (pt0) cc_final: 0.8340 (pm20) REVERT: N 82 ASP cc_start: 0.8691 (m-30) cc_final: 0.7797 (m-30) REVERT: N 85 GLU cc_start: 0.7886 (tp30) cc_final: 0.7545 (tp30) REVERT: N 103 LYS cc_start: 0.8676 (tppp) cc_final: 0.8396 (tppt) outliers start: 53 outliers final: 16 residues processed: 329 average time/residue: 0.6635 time to fit residues: 242.8885 Evaluate side-chains 310 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 ARG Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 113 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain N residue 31 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: [192, 227, 214, 23, 182, 2, 189, 82, 210, 229, 231] chunk 192 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 397 HIS C 182 ASN O 113 GLN J 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.071785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.047193 restraints weight = 56421.544| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.70 r_work: 0.2603 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19686 Z= 0.196 Angle : 0.657 10.230 26745 Z= 0.332 Chirality : 0.044 0.161 2943 Planarity : 0.004 0.055 3357 Dihedral : 4.802 25.182 2859 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.94 % Allowed : 16.88 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2403 helix: 1.05 (0.35), residues: 198 sheet: 0.58 (0.18), residues: 783 loop : -0.13 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 40 TYR 0.023 0.002 TYR L 49 PHE 0.013 0.001 PHE I 79 TRP 0.008 0.001 TRP E 35 HIS 0.003 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (19644) covalent geometry : angle 0.65539 / 0.33 (26652) SS BOND : bond 0.00270 / 0.19 ( 33) SS BOND : angle 0.97806 / 0.66 ( 66) hydrogen bonds : bond 0.03546 / 2.41 ( 632) hydrogen bonds : angle 5.56850 / 3.92 ( 1596) link_NAG-ASN : bond 0.00061 / 0.04 ( 9) link_NAG-ASN : angle 1.18567 / 0.74 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 304 time to evaluate : 0.730 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: F 12 ASP cc_start: 0.8865 (t0) cc_final: 0.8331 (t70) REVERT: F 13 THR cc_start: 0.9744 (m) cc_final: 0.9360 (t) REVERT: F 16 GLN cc_start: 0.9127 (mp10) cc_final: 0.8843 (mp10) REVERT: F 54 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8681 (ttmm) REVERT: F 83 ASP cc_start: 0.7254 (m-30) cc_final: 0.7028 (m-30) REVERT: F 84 GLU cc_start: 0.9154 (pp20) cc_final: 0.8803 (pm20) REVERT: M 4 GLN cc_start: 0.6865 (pm20) cc_final: 0.6659 (pm20) REVERT: M 24 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8150 (ttpp) REVERT: M 47 GLU cc_start: 0.8511 (pm20) cc_final: 0.8131 (pm20) REVERT: M 87 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8688 (mm) REVERT: B 102 MET cc_start: 0.8732 (mmp) cc_final: 0.8234 (mmm) REVERT: D 12 ASP cc_start: 0.8672 (t0) cc_final: 0.7858 (t0) REVERT: D 16 GLN cc_start: 0.8632 (mp10) cc_final: 0.8307 (pm20) REVERT: D 83 ASP cc_start: 0.7691 (m-30) cc_final: 0.6977 (m-30) REVERT: H 12 ASP cc_start: 0.8833 (t0) cc_final: 0.7937 (t0) REVERT: H 13 THR cc_start: 0.9715 (m) cc_final: 0.9366 (t) REVERT: H 16 GLN cc_start: 0.9046 (mp10) cc_final: 0.8552 (mp10) REVERT: H 17 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8428 (ttp80) REVERT: H 18 VAL cc_start: 0.8076 (p) cc_final: 0.7781 (m) REVERT: H 54 LYS cc_start: 0.9284 (mmtp) cc_final: 0.8768 (mmmm) REVERT: H 62 ARG cc_start: 0.9155 (ptp90) cc_final: 0.8825 (ptp90) REVERT: A 56 MET cc_start: 0.8378 (tpp) cc_final: 0.8023 (mtp) REVERT: A 281 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8638 (mm-30) REVERT: A 368 ASP cc_start: 0.9378 (m-30) cc_final: 0.9151 (p0) REVERT: I 2 GLN cc_start: 0.9002 (tp40) cc_final: 0.8267 (tp-100) REVERT: I 28 ASP cc_start: 0.8637 (t0) cc_final: 0.8371 (t0) REVERT: I 44 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8730 (mmtt) REVERT: I 65 LYS cc_start: 0.9313 (ttmm) cc_final: 0.9082 (ttmm) REVERT: I 76 LYS cc_start: 0.9626 (mtpm) cc_final: 0.9389 (mtmm) REVERT: E 76 LYS cc_start: 0.9679 (mtpp) cc_final: 0.9425 (mtmm) REVERT: E 84 ASN cc_start: 0.9322 (t0) cc_final: 0.9086 (m110) REVERT: K 14 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6994 (tpm170) REVERT: K 64 LYS cc_start: 0.9444 (ttpt) cc_final: 0.9091 (ttpt) REVERT: K 86 ARG cc_start: 0.9171 (mmp80) cc_final: 0.8884 (mmp80) REVERT: O 4 GLN cc_start: 0.7677 (pp30) cc_final: 0.7321 (pp30) REVERT: O 24 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7680 (ttmm) REVERT: O 39 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8446 (tttp) REVERT: O 45 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7572 (tpp80) REVERT: O 66 LYS cc_start: 0.9155 (tppt) cc_final: 0.8550 (mmmt) REVERT: O 86 ARG cc_start: 0.9581 (OUTLIER) cc_final: 0.9202 (mpp80) REVERT: O 113 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.9106 (pm20) REVERT: O 116 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8933 (tm) REVERT: L 24 LYS cc_start: 0.9349 (ttmm) cc_final: 0.9070 (tppp) REVERT: L 27 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7908 (tm-30) REVERT: L 49 TYR cc_start: 0.8385 (p90) cc_final: 0.8121 (p90) REVERT: L 85 GLU cc_start: 0.7834 (tp30) cc_final: 0.7529 (tp30) REVERT: L 87 PHE cc_start: 0.8772 (m-80) cc_final: 0.8202 (m-80) REVERT: L 103 LYS cc_start: 0.8475 (tppp) cc_final: 0.8105 (tppt) REVERT: J 8 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7804 (tp-100) REVERT: J 11 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7777 (mtt) REVERT: J 24 LYS cc_start: 0.8816 (mppt) cc_final: 0.8508 (mppt) REVERT: J 49 TYR cc_start: 0.8581 (p90) cc_final: 0.8282 (p90) REVERT: J 82 ASP cc_start: 0.8848 (m-30) cc_final: 0.8484 (m-30) REVERT: J 85 GLU cc_start: 0.7958 (mp0) cc_final: 0.7591 (mp0) REVERT: N 77 ASN cc_start: 0.8790 (t0) cc_final: 0.8430 (t0) REVERT: N 81 GLU cc_start: 0.8806 (pt0) cc_final: 0.8444 (pm20) REVERT: N 85 GLU cc_start: 0.7942 (tp30) cc_final: 0.7602 (tp30) REVERT: N 103 LYS cc_start: 0.8674 (tppp) cc_final: 0.8403 (tppt) outliers start: 62 outliers final: 25 residues processed: 335 average time/residue: 0.6446 time to fit residues: 241.1630 Evaluate side-chains 320 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 86 ARG Chi-restraints excluded: chain O residue 113 GLN Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: [127, 1, 0, 156, 100, 96, 175, 170, 55, 159, 92] chunk 127 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 397 HIS A 21 HIS ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.071481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.046939 restraints weight = 56279.401| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.69 r_work: 0.2598 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19686 Z= 0.216 Angle : 0.679 11.321 26745 Z= 0.342 Chirality : 0.044 0.195 2943 Planarity : 0.004 0.054 3357 Dihedral : 4.773 22.092 2859 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.94 % Allowed : 18.07 % Favored : 78.99 % 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: 0.23 (0.17), residues: 2403 helix: 1.11 (0.36), residues: 198 sheet: 0.60 (0.18), residues: 795 loop : -0.20 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 45 TYR 0.025 0.002 TYR L 49 PHE 0.014 0.001 PHE I 79 TRP 0.008 0.001 TRP C 100 HIS 0.003 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (19644) covalent geometry : angle 0.67690 / 0.34 (26652) SS BOND : bond 0.00277 / 0.20 ( 33) SS BOND : angle 0.98270 / 0.67 ( 66) hydrogen bonds : bond 0.03530 / 2.39 ( 632) hydrogen bonds : angle 5.53271 / 3.89 ( 1596) link_NAG-ASN : bond 0.00078 / 0.05 ( 9) link_NAG-ASN : angle 1.23943 / 0.78 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 299 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.8836 (t0) cc_final: 0.8335 (t0) REVERT: F 13 THR cc_start: 0.9747 (m) cc_final: 0.9393 (t) REVERT: F 16 GLN cc_start: 0.9095 (mp10) cc_final: 0.8826 (mp10) REVERT: F 54 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.8708 (ttmm) REVERT: F 83 ASP cc_start: 0.7308 (m-30) cc_final: 0.7103 (m-30) REVERT: F 84 GLU cc_start: 0.9161 (pp20) cc_final: 0.8779 (pm20) REVERT: M 4 GLN cc_start: 0.6915 (pm20) cc_final: 0.6710 (pm20) REVERT: M 24 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8178 (ttpp) REVERT: M 47 GLU cc_start: 0.8453 (pm20) cc_final: 0.8105 (pm20) REVERT: M 87 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8846 (mm) REVERT: B 56 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7860 (mtp) REVERT: B 102 MET cc_start: 0.8717 (mmp) cc_final: 0.8244 (mmm) REVERT: D 12 ASP cc_start: 0.8673 (t0) cc_final: 0.8048 (t0) REVERT: D 17 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8116 (ptm-80) REVERT: D 62 ARG cc_start: 0.9160 (ptt-90) cc_final: 0.8930 (ptt-90) REVERT: D 100 LEU cc_start: 0.9029 (mp) cc_final: 0.8766 (mt) REVERT: H 12 ASP cc_start: 0.8728 (t0) cc_final: 0.8160 (t70) REVERT: H 13 THR cc_start: 0.9695 (m) cc_final: 0.9292 (t) REVERT: H 16 GLN cc_start: 0.9038 (mp10) cc_final: 0.8647 (mp10) REVERT: H 17 ARG cc_start: 0.9041 (ttp80) cc_final: 0.8499 (ttp80) REVERT: H 46 LYS cc_start: 0.9072 (tmmm) cc_final: 0.8534 (tmmm) REVERT: H 54 LYS cc_start: 0.9346 (mmtp) cc_final: 0.8854 (mmmm) REVERT: C 278 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8836 (mmtt) REVERT: A 175 TYR cc_start: 0.9158 (m-10) cc_final: 0.8937 (m-10) REVERT: A 281 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8644 (mm-30) REVERT: I 2 GLN cc_start: 0.8996 (tp40) cc_final: 0.8296 (tp-100) REVERT: I 28 ASP cc_start: 0.8652 (t0) cc_final: 0.8387 (t0) REVERT: I 76 LYS cc_start: 0.9622 (mtpm) cc_final: 0.9382 (mtmm) REVERT: E 76 LYS cc_start: 0.9674 (mtpp) cc_final: 0.9424 (mtmm) REVERT: E 84 ASN cc_start: 0.9323 (t0) cc_final: 0.9079 (m110) REVERT: K 14 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7208 (tpm170) REVERT: K 47 GLU cc_start: 0.8026 (pm20) cc_final: 0.7718 (pm20) REVERT: K 64 LYS cc_start: 0.9425 (ttpt) cc_final: 0.9077 (ttpt) REVERT: K 86 ARG cc_start: 0.9195 (mmp80) cc_final: 0.8920 (mmp80) REVERT: O 4 GLN cc_start: 0.7843 (pp30) cc_final: 0.7547 (pp30) REVERT: O 24 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7711 (ttmm) REVERT: O 39 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8455 (tttp) REVERT: O 45 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7590 (tpp80) REVERT: O 113 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.9125 (pm20) REVERT: O 116 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8942 (tm) REVERT: L 24 LYS cc_start: 0.9346 (ttmm) cc_final: 0.8907 (tppp) REVERT: L 27 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7935 (tm-30) REVERT: L 40 ARG cc_start: 0.8880 (tmm-80) cc_final: 0.8494 (tmm-80) REVERT: L 49 TYR cc_start: 0.8400 (p90) cc_final: 0.8144 (p90) REVERT: L 77 ASN cc_start: 0.8372 (t0) cc_final: 0.8157 (t0) REVERT: L 85 GLU cc_start: 0.7803 (tp30) cc_final: 0.7571 (tp30) REVERT: L 103 LYS cc_start: 0.8492 (tppp) cc_final: 0.8113 (tppt) REVERT: J 8 GLN cc_start: 0.8230 (tp-100) cc_final: 0.7971 (tp-100) REVERT: J 11 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8000 (mtt) REVERT: J 24 LYS cc_start: 0.8851 (mppt) cc_final: 0.8518 (mppt) REVERT: J 49 TYR cc_start: 0.8609 (p90) cc_final: 0.8349 (p90) REVERT: J 63 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8687 (p) REVERT: J 82 ASP cc_start: 0.8788 (m-30) cc_final: 0.8458 (m-30) REVERT: J 85 GLU cc_start: 0.7979 (mp0) cc_final: 0.7624 (mp0) REVERT: J 103 LYS cc_start: 0.8506 (tppp) cc_final: 0.8087 (tppt) REVERT: N 40 ARG cc_start: 0.8854 (tmm-80) cc_final: 0.8648 (ttp80) REVERT: N 77 ASN cc_start: 0.8841 (t0) cc_final: 0.8539 (t0) REVERT: N 81 GLU cc_start: 0.8856 (pt0) cc_final: 0.8466 (pm20) REVERT: N 85 GLU cc_start: 0.7993 (tp30) cc_final: 0.7584 (tp30) REVERT: N 103 LYS cc_start: 0.8783 (tppp) cc_final: 0.8426 (tppt) outliers start: 62 outliers final: 31 residues processed: 334 average time/residue: 0.6350 time to fit residues: 237.4453 Evaluate side-chains 322 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 113 GLN Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain N residue 31 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: [86, 158, 103, 25, 20, 54, 49, 80, 140, 47, 46] chunk 86 optimal weight: 8.9990 chunk 158 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 384 HIS A 397 HIS O 113 GLN J 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.048753 restraints weight = 55967.658| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.71 r_work: 0.2646 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19686 Z= 0.123 Angle : 0.656 11.470 26745 Z= 0.325 Chirality : 0.043 0.195 2943 Planarity : 0.004 0.054 3357 Dihedral : 4.449 19.585 2859 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.37 % Allowed : 19.16 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2403 helix: 1.95 (0.37), residues: 180 sheet: 0.66 (0.18), residues: 783 loop : -0.17 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 45 TYR 0.024 0.001 TYR D 50 PHE 0.012 0.001 PHE A 59 TRP 0.011 0.001 TRP C 100 HIS 0.003 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (19644) covalent geometry : angle 0.65573 / 0.32 (26652) SS BOND : bond 0.00229 / 0.16 ( 33) SS BOND : angle 0.74877 / 0.50 ( 66) hydrogen bonds : bond 0.03100 / 2.09 ( 632) hydrogen bonds : angle 5.29417 / 3.74 ( 1596) link_NAG-ASN : bond 0.00082 / 0.05 ( 9) link_NAG-ASN : angle 1.04298 / 0.65 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 320 time to evaluate : 0.750 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: F 12 ASP cc_start: 0.8678 (t0) cc_final: 0.8123 (t70) REVERT: F 13 THR cc_start: 0.9736 (m) cc_final: 0.9327 (t) REVERT: F 16 GLN cc_start: 0.9113 (mp10) cc_final: 0.8844 (mp10) REVERT: F 54 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.8721 (ttmm) REVERT: F 84 GLU cc_start: 0.9172 (pp20) cc_final: 0.8866 (pm20) REVERT: M 4 GLN cc_start: 0.6902 (pm20) cc_final: 0.6687 (pm20) REVERT: M 24 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8149 (ttpp) REVERT: M 39 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.7924 (tttp) REVERT: M 47 GLU cc_start: 0.8429 (pm20) cc_final: 0.8069 (pm20) REVERT: M 87 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8869 (mm) REVERT: M 116 LEU cc_start: 0.9289 (tt) cc_final: 0.9080 (tm) REVERT: B 102 MET cc_start: 0.8744 (mmp) cc_final: 0.8342 (mmm) REVERT: B 175 TYR cc_start: 0.8985 (m-80) cc_final: 0.8655 (m-80) REVERT: B 187 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7240 (ptt) REVERT: D 12 ASP cc_start: 0.8570 (t0) cc_final: 0.8057 (t0) REVERT: D 13 THR cc_start: 0.9728 (OUTLIER) cc_final: 0.9504 (t) REVERT: D 16 GLN cc_start: 0.8948 (mp10) cc_final: 0.8699 (mp10) REVERT: D 17 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8244 (ptm-80) REVERT: D 83 ASP cc_start: 0.7858 (m-30) cc_final: 0.7247 (m-30) REVERT: D 84 GLU cc_start: 0.8991 (pp20) cc_final: 0.8693 (pm20) REVERT: D 100 LEU cc_start: 0.9032 (mp) cc_final: 0.8735 (mt) REVERT: H 12 ASP cc_start: 0.8638 (t0) cc_final: 0.7652 (t70) REVERT: H 13 THR cc_start: 0.9729 (m) cc_final: 0.9324 (t) REVERT: H 16 GLN cc_start: 0.9119 (mp10) cc_final: 0.8655 (mp10) REVERT: H 17 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8546 (ttp80) REVERT: H 18 VAL cc_start: 0.8066 (p) cc_final: 0.7739 (m) REVERT: H 46 LYS cc_start: 0.9020 (tmmm) cc_final: 0.8486 (tmmm) REVERT: H 54 LYS cc_start: 0.9348 (mmtp) cc_final: 0.8854 (mmmm) REVERT: H 84 GLU cc_start: 0.9026 (pp20) cc_final: 0.8493 (pm20) REVERT: C 175 TYR cc_start: 0.8980 (m-80) cc_final: 0.8615 (m-80) REVERT: C 278 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8794 (mmtt) REVERT: A 56 MET cc_start: 0.8409 (tpp) cc_final: 0.8099 (mtp) REVERT: A 175 TYR cc_start: 0.9155 (m-10) cc_final: 0.8943 (m-10) REVERT: A 281 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8592 (mm-30) REVERT: A 368 ASP cc_start: 0.8605 (p0) cc_final: 0.8055 (p0) REVERT: I 2 GLN cc_start: 0.8979 (tp40) cc_final: 0.8294 (tp-100) REVERT: I 28 ASP cc_start: 0.8684 (t0) cc_final: 0.8384 (t0) REVERT: I 76 LYS cc_start: 0.9643 (OUTLIER) cc_final: 0.9422 (mtmm) REVERT: E 76 LYS cc_start: 0.9662 (mtpp) cc_final: 0.9370 (mtmm) REVERT: E 84 ASN cc_start: 0.9285 (t0) cc_final: 0.9075 (m110) REVERT: K 14 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7185 (tpm170) REVERT: K 86 ARG cc_start: 0.9199 (mmp80) cc_final: 0.8938 (mmp80) REVERT: O 24 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7821 (ttmm) REVERT: O 39 LYS cc_start: 0.8873 (ttpp) cc_final: 0.8417 (tttp) REVERT: O 45 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7531 (tpp80) REVERT: O 64 LYS cc_start: 0.9371 (ttpp) cc_final: 0.9110 (ttpp) REVERT: O 68 LYS cc_start: 0.8743 (tppt) cc_final: 0.8181 (tppt) REVERT: O 86 ARG cc_start: 0.9225 (mpp80) cc_final: 0.8465 (mpp80) REVERT: O 113 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8616 (pm20) REVERT: O 116 LEU cc_start: 0.9265 (tt) cc_final: 0.8970 (tm) REVERT: L 27 GLN cc_start: 0.8244 (tm-30) cc_final: 0.8003 (tm-30) REVERT: L 40 ARG cc_start: 0.8922 (tmm-80) cc_final: 0.8558 (tmm-80) REVERT: L 49 TYR cc_start: 0.8196 (p90) cc_final: 0.7739 (p90) REVERT: L 63 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8371 (p) REVERT: L 77 ASN cc_start: 0.8317 (t0) cc_final: 0.8068 (t0) REVERT: L 85 GLU cc_start: 0.7726 (tp30) cc_final: 0.7402 (tp30) REVERT: L 103 LYS cc_start: 0.8479 (tppp) cc_final: 0.8156 (tppt) REVERT: J 11 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8298 (mtm) REVERT: J 49 TYR cc_start: 0.8447 (p90) cc_final: 0.7814 (p90) REVERT: J 63 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8694 (p) REVERT: J 82 ASP cc_start: 0.8776 (m-30) cc_final: 0.8399 (m-30) REVERT: J 85 GLU cc_start: 0.7975 (mp0) cc_final: 0.7605 (mp0) REVERT: N 27 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8126 (tm-30) REVERT: N 40 ARG cc_start: 0.8837 (tmm-80) cc_final: 0.8620 (ttp80) REVERT: N 77 ASN cc_start: 0.8772 (t0) cc_final: 0.8472 (t0) REVERT: N 81 GLU cc_start: 0.8850 (pt0) cc_final: 0.8494 (pm20) REVERT: N 82 ASP cc_start: 0.8469 (m-30) cc_final: 0.7978 (m-30) REVERT: N 85 GLU cc_start: 0.7970 (tp30) cc_final: 0.7521 (tp30) REVERT: N 103 LYS cc_start: 0.8709 (tppp) cc_final: 0.8378 (tppt) outliers start: 50 outliers final: 27 residues processed: 352 average time/residue: 0.6057 time to fit residues: 239.4487 Evaluate side-chains 338 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 298 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 113 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: [159, 139, 5, 163, 91, 19, 225, 167, 168, 29, 232] chunk 159 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS A 377 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN L 32 ASN J 32 ASN J 37 GLN N 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.070707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.046163 restraints weight = 56552.616| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.68 r_work: 0.2577 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 19686 Z= 0.278 Angle : 0.728 11.544 26745 Z= 0.367 Chirality : 0.045 0.220 2943 Planarity : 0.005 0.054 3357 Dihedral : 4.828 21.354 2859 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.23 % Allowed : 20.01 % Favored : 77.76 % 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: 0.16 (0.17), residues: 2403 helix: 0.95 (0.34), residues: 216 sheet: 0.57 (0.17), residues: 817 loop : -0.26 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 45 TYR 0.031 0.002 TYR L 49 PHE 0.017 0.002 PHE I 79 TRP 0.008 0.001 TRP A 100 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.28 (19644) covalent geometry : angle 0.72587 / 0.37 (26652) SS BOND : bond 0.00324 / 0.23 ( 33) SS BOND : angle 1.10061 / 0.75 ( 66) hydrogen bonds : bond 0.03641 / 2.46 ( 632) hydrogen bonds : angle 5.51015 / 3.88 ( 1596) link_NAG-ASN : bond 0.00143 / 0.08 ( 9) link_NAG-ASN : angle 1.37704 / 0.86 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 293 time to evaluate : 0.711 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: F 12 ASP cc_start: 0.8830 (t0) cc_final: 0.8270 (t70) REVERT: F 13 THR cc_start: 0.9751 (m) cc_final: 0.9353 (t) REVERT: F 16 GLN cc_start: 0.9141 (mp10) cc_final: 0.8868 (mp10) REVERT: F 46 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8392 (tmmm) REVERT: F 54 LYS cc_start: 0.9490 (OUTLIER) cc_final: 0.8727 (ttmm) REVERT: F 84 GLU cc_start: 0.9167 (pp20) cc_final: 0.8829 (pm20) REVERT: M 24 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8186 (ttpp) REVERT: M 39 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.7904 (tttp) REVERT: M 47 GLU cc_start: 0.8436 (pm20) cc_final: 0.8136 (pm20) REVERT: M 84 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8248 (mm) REVERT: M 87 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8918 (mm) REVERT: B 102 MET cc_start: 0.8761 (mmp) cc_final: 0.8298 (mmm) REVERT: B 175 TYR cc_start: 0.9121 (m-80) cc_final: 0.8863 (m-80) REVERT: D 12 ASP cc_start: 0.8580 (t0) cc_final: 0.7969 (t0) REVERT: D 13 THR cc_start: 0.9678 (OUTLIER) cc_final: 0.9381 (t) REVERT: D 16 GLN cc_start: 0.9012 (mp10) cc_final: 0.8777 (mp10) REVERT: D 17 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8323 (ptm-80) REVERT: H 12 ASP cc_start: 0.8639 (t0) cc_final: 0.7991 (t70) REVERT: H 13 THR cc_start: 0.9729 (m) cc_final: 0.9348 (t) REVERT: H 16 GLN cc_start: 0.9039 (mp10) cc_final: 0.8669 (mp10) REVERT: H 17 ARG cc_start: 0.9108 (ttp80) cc_final: 0.8604 (ttp80) REVERT: H 46 LYS cc_start: 0.9073 (tmmm) cc_final: 0.8514 (tmmm) REVERT: H 54 LYS cc_start: 0.9385 (mmtp) cc_final: 0.8910 (mmmm) REVERT: H 84 GLU cc_start: 0.9006 (pp20) cc_final: 0.8485 (pm20) REVERT: C 278 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8797 (mmtt) REVERT: A 281 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8669 (mm-30) REVERT: A 368 ASP cc_start: 0.8599 (p0) cc_final: 0.8063 (p0) REVERT: I 2 GLN cc_start: 0.9033 (tp40) cc_final: 0.8349 (tp-100) REVERT: I 28 ASP cc_start: 0.8607 (t0) cc_final: 0.8337 (t0) REVERT: I 76 LYS cc_start: 0.9625 (mtpm) cc_final: 0.9382 (mtmm) REVERT: E 84 ASN cc_start: 0.9380 (t0) cc_final: 0.9086 (m110) REVERT: K 12 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8762 (tm) REVERT: K 14 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7267 (tpm170) REVERT: K 64 LYS cc_start: 0.9314 (ttpt) cc_final: 0.8990 (ttpt) REVERT: K 86 ARG cc_start: 0.9239 (mmp80) cc_final: 0.9012 (mmp80) REVERT: O 24 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7793 (ttmm) REVERT: O 39 LYS cc_start: 0.8835 (ttpp) cc_final: 0.8404 (tttp) REVERT: O 45 ARG cc_start: 0.8288 (tpp80) cc_final: 0.7616 (tpp80) REVERT: O 113 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8777 (pm20) REVERT: O 116 LEU cc_start: 0.9255 (tt) cc_final: 0.8962 (tm) REVERT: L 27 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7983 (tm-30) REVERT: L 40 ARG cc_start: 0.8972 (tmm-80) cc_final: 0.8592 (tmm-80) REVERT: L 63 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8473 (p) REVERT: L 77 ASN cc_start: 0.8332 (t0) cc_final: 0.8079 (t0) REVERT: L 85 GLU cc_start: 0.7793 (tp30) cc_final: 0.7534 (tp30) REVERT: L 103 LYS cc_start: 0.8483 (tppp) cc_final: 0.8142 (tppt) REVERT: J 11 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8391 (mtm) REVERT: J 82 ASP cc_start: 0.8837 (m-30) cc_final: 0.8460 (m-30) REVERT: J 85 GLU cc_start: 0.7991 (mp0) cc_final: 0.7656 (mp0) REVERT: N 77 ASN cc_start: 0.8860 (t0) cc_final: 0.8545 (t0) REVERT: N 81 GLU cc_start: 0.8855 (pt0) cc_final: 0.8496 (pm20) REVERT: N 85 GLU cc_start: 0.8022 (tp30) cc_final: 0.7344 (tp30) outliers start: 47 outliers final: 24 residues processed: 320 average time/residue: 0.6472 time to fit residues: 230.7972 Evaluate side-chains 316 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 113 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: [200, 41, 91, 76, 206, 137, 93, 143, 63, 96, 45] chunk 200 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.048456 restraints weight = 55797.919| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.69 r_work: 0.2639 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19686 Z= 0.137 Angle : 0.710 12.510 26745 Z= 0.351 Chirality : 0.043 0.198 2943 Planarity : 0.005 0.086 3357 Dihedral : 4.524 19.094 2859 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.28 % Allowed : 20.15 % Favored : 77.57 % 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: 0.31 (0.17), residues: 2403 helix: 1.21 (0.35), residues: 216 sheet: 0.81 (0.18), residues: 783 loop : -0.27 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 40 TYR 0.021 0.001 TYR D 50 PHE 0.009 0.001 PHE I 79 TRP 0.012 0.001 TRP A 100 HIS 0.003 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (19644) covalent geometry : angle 0.70950 / 0.35 (26652) SS BOND : bond 0.00238 / 0.16 ( 33) SS BOND : angle 0.78053 / 0.52 ( 66) hydrogen bonds : bond 0.03077 / 2.07 ( 632) hydrogen bonds : angle 5.26538 / 3.72 ( 1596) link_NAG-ASN : bond 0.00080 / 0.05 ( 9) link_NAG-ASN : angle 1.06472 / 0.67 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 309 time to evaluate : 0.754 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: F 12 ASP cc_start: 0.8670 (t0) cc_final: 0.8118 (t70) REVERT: F 13 THR cc_start: 0.9730 (m) cc_final: 0.9304 (t) REVERT: F 16 GLN cc_start: 0.9156 (mp10) cc_final: 0.8907 (mp10) REVERT: F 54 LYS cc_start: 0.9475 (OUTLIER) cc_final: 0.8842 (ttmm) REVERT: F 84 GLU cc_start: 0.9118 (pp20) cc_final: 0.8812 (pm20) REVERT: M 11 GLU cc_start: 0.8268 (pm20) cc_final: 0.7979 (mp0) REVERT: M 24 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8162 (ttpp) REVERT: M 39 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.7897 (tttp) REVERT: M 47 GLU cc_start: 0.8441 (pm20) cc_final: 0.8073 (pm20) REVERT: M 87 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8782 (mm) REVERT: B 102 MET cc_start: 0.8730 (mmp) cc_final: 0.8289 (mmm) REVERT: B 175 TYR cc_start: 0.9115 (m-80) cc_final: 0.8829 (m-80) REVERT: B 291 MET cc_start: 0.7866 (mmm) cc_final: 0.7512 (mmt) REVERT: D 12 ASP cc_start: 0.8386 (t0) cc_final: 0.7677 (t0) REVERT: D 13 THR cc_start: 0.9719 (OUTLIER) cc_final: 0.9452 (t) REVERT: D 17 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8278 (ptm-80) REVERT: D 83 ASP cc_start: 0.7864 (m-30) cc_final: 0.7443 (m-30) REVERT: D 84 GLU cc_start: 0.9076 (pp20) cc_final: 0.8709 (pm20) REVERT: D 100 LEU cc_start: 0.9103 (mp) cc_final: 0.8814 (mt) REVERT: H 12 ASP cc_start: 0.8484 (t0) cc_final: 0.7837 (t70) REVERT: H 13 THR cc_start: 0.9726 (m) cc_final: 0.9318 (t) REVERT: H 16 GLN cc_start: 0.9054 (mp10) cc_final: 0.8678 (mp10) REVERT: H 17 ARG cc_start: 0.9148 (ttp80) cc_final: 0.8666 (ttp80) REVERT: H 46 LYS cc_start: 0.9018 (tmmm) cc_final: 0.8465 (tmmm) REVERT: H 54 LYS cc_start: 0.9387 (mmtp) cc_final: 0.8906 (mmmm) REVERT: H 84 GLU cc_start: 0.9035 (pp20) cc_final: 0.8581 (pm20) REVERT: C 175 TYR cc_start: 0.8900 (m-80) cc_final: 0.8554 (m-80) REVERT: C 278 LYS cc_start: 0.9091 (mmmt) cc_final: 0.8835 (mmtt) REVERT: A 56 MET cc_start: 0.8459 (tpp) cc_final: 0.8254 (mmt) REVERT: A 281 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8584 (mm-30) REVERT: A 368 ASP cc_start: 0.8666 (p0) cc_final: 0.8160 (p0) REVERT: I 2 GLN cc_start: 0.8973 (tp40) cc_final: 0.8331 (tp-100) REVERT: I 28 ASP cc_start: 0.8714 (t0) cc_final: 0.8421 (t0) REVERT: I 76 LYS cc_start: 0.9641 (OUTLIER) cc_final: 0.9438 (mtmm) REVERT: E 76 LYS cc_start: 0.9661 (mtpp) cc_final: 0.9418 (mtmm) REVERT: E 84 ASN cc_start: 0.9295 (t0) cc_final: 0.9065 (m110) REVERT: K 4 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7628 (tm130) REVERT: K 11 GLU cc_start: 0.8600 (pm20) cc_final: 0.8244 (mp0) REVERT: K 14 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7233 (tpm170) REVERT: K 64 LYS cc_start: 0.9308 (ttpt) cc_final: 0.8987 (ttpt) REVERT: K 86 ARG cc_start: 0.9217 (mmp80) cc_final: 0.8948 (mmp80) REVERT: O 24 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7768 (ttmm) REVERT: O 45 ARG cc_start: 0.8323 (tpp80) cc_final: 0.7632 (tpp80) REVERT: O 64 LYS cc_start: 0.9364 (ttpp) cc_final: 0.9106 (ttpp) REVERT: O 66 LYS cc_start: 0.9166 (tppt) cc_final: 0.8537 (mmmt) REVERT: O 113 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8616 (pm20) REVERT: O 116 LEU cc_start: 0.9340 (tt) cc_final: 0.9103 (tm) REVERT: L 27 GLN cc_start: 0.8269 (tm-30) cc_final: 0.8027 (tm-30) REVERT: L 49 TYR cc_start: 0.8251 (p90) cc_final: 0.7808 (p90) REVERT: L 53 TYR cc_start: 0.8830 (m-80) cc_final: 0.8609 (m-80) REVERT: L 63 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8510 (p) REVERT: L 77 ASN cc_start: 0.8282 (t0) cc_final: 0.7997 (t0) REVERT: L 85 GLU cc_start: 0.7759 (tp30) cc_final: 0.7415 (tp30) REVERT: L 103 LYS cc_start: 0.8433 (tppp) cc_final: 0.8106 (tppt) REVERT: J 63 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8752 (p) REVERT: J 77 ASN cc_start: 0.8489 (t0) cc_final: 0.8261 (t0) REVERT: J 82 ASP cc_start: 0.8837 (m-30) cc_final: 0.8461 (m-30) REVERT: J 85 GLU cc_start: 0.7959 (mp0) cc_final: 0.7571 (mp0) REVERT: N 27 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8135 (tm-30) REVERT: N 77 ASN cc_start: 0.8684 (t0) cc_final: 0.8243 (t0) REVERT: N 79 GLN cc_start: 0.7376 (mp10) cc_final: 0.6985 (mp10) REVERT: N 81 GLU cc_start: 0.8944 (pt0) cc_final: 0.8594 (pm20) REVERT: N 85 GLU cc_start: 0.7964 (tp30) cc_final: 0.7495 (tp30) REVERT: N 103 LYS cc_start: 0.8717 (tppp) cc_final: 0.8349 (tppt) outliers start: 48 outliers final: 23 residues processed: 337 average time/residue: 0.6185 time to fit residues: 233.2849 Evaluate side-chains 333 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 113 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: [193, 215, 234, 178, 148, 103, 0, 28, 202, 92, 133] chunk 193 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.071252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.046878 restraints weight = 56120.390| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.66 r_work: 0.2591 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19686 Z= 0.230 Angle : 0.753 12.785 26745 Z= 0.376 Chirality : 0.045 0.218 2943 Planarity : 0.004 0.059 3357 Dihedral : 4.732 21.724 2859 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.85 % Allowed : 20.53 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.17), residues: 2403 helix: 1.07 (0.35), residues: 216 sheet: 0.60 (0.17), residues: 807 loop : -0.29 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 45 TYR 0.028 0.002 TYR L 49 PHE 0.014 0.001 PHE I 79 TRP 0.010 0.001 TRP A 100 HIS 0.004 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (19644) covalent geometry : angle 0.75111 / 0.38 (26652) SS BOND : bond 0.00291 / 0.21 ( 33) SS BOND : angle 1.03549 / 0.71 ( 66) hydrogen bonds : bond 0.03470 / 2.33 ( 632) hydrogen bonds : angle 5.40472 / 3.82 ( 1596) link_NAG-ASN : bond 0.00099 / 0.06 ( 9) link_NAG-ASN : angle 1.30806 / 0.82 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4806 Ramachandran restraints generated. 2403 Oldfield, 0 Emsley, 2403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 292 time to evaluate : 0.759 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: F 12 ASP cc_start: 0.8753 (t0) cc_final: 0.8211 (t70) REVERT: F 13 THR cc_start: 0.9723 (m) cc_final: 0.9316 (t) REVERT: F 54 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.8700 (ttmm) REVERT: F 84 GLU cc_start: 0.9254 (pp20) cc_final: 0.8901 (pm20) REVERT: M 11 GLU cc_start: 0.8280 (pm20) cc_final: 0.7906 (mp0) REVERT: M 24 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8213 (ttpp) REVERT: M 39 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.7906 (tttp) REVERT: M 47 GLU cc_start: 0.8420 (pm20) cc_final: 0.8097 (pm20) REVERT: M 84 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8287 (mm) REVERT: M 86 ARG cc_start: 0.8607 (mpp80) cc_final: 0.8282 (mpp80) REVERT: M 87 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8767 (mm) REVERT: G 30 MET cc_start: 0.9233 (mmm) cc_final: 0.7957 (mmm) REVERT: B 102 MET cc_start: 0.8749 (mmp) cc_final: 0.8295 (mmm) REVERT: B 175 TYR cc_start: 0.9104 (m-80) cc_final: 0.8872 (m-80) REVERT: D 12 ASP cc_start: 0.8504 (t0) cc_final: 0.7778 (t0) REVERT: D 13 THR cc_start: 0.9724 (OUTLIER) cc_final: 0.9461 (t) REVERT: D 16 GLN cc_start: 0.9044 (mp10) cc_final: 0.8826 (mp10) REVERT: D 17 ARG cc_start: 0.8840 (ttp80) cc_final: 0.8370 (ptm-80) REVERT: D 100 LEU cc_start: 0.9030 (mp) cc_final: 0.8821 (mt) REVERT: H 12 ASP cc_start: 0.8529 (t0) cc_final: 0.7521 (t70) REVERT: H 13 THR cc_start: 0.9747 (m) cc_final: 0.9337 (t) REVERT: H 16 GLN cc_start: 0.9056 (mp10) cc_final: 0.8574 (mp10) REVERT: H 17 ARG cc_start: 0.9160 (ttp80) cc_final: 0.8657 (ttp80) REVERT: H 18 VAL cc_start: 0.7933 (OUTLIER) cc_final: 0.7671 (m) REVERT: H 54 LYS cc_start: 0.9408 (mmtp) cc_final: 0.8967 (mmmm) REVERT: H 84 GLU cc_start: 0.9025 (pp20) cc_final: 0.8559 (pm20) REVERT: C 175 TYR cc_start: 0.8990 (m-80) cc_final: 0.8617 (m-80) REVERT: C 278 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8843 (mmtt) REVERT: A 281 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8638 (mm-30) REVERT: A 368 ASP cc_start: 0.8614 (p0) cc_final: 0.8082 (p0) REVERT: I 2 GLN cc_start: 0.8986 (tp40) cc_final: 0.8356 (tp-100) REVERT: I 28 ASP cc_start: 0.8705 (t0) cc_final: 0.8417 (t0) REVERT: I 76 LYS cc_start: 0.9645 (OUTLIER) cc_final: 0.9431 (mtmm) REVERT: E 76 LYS cc_start: 0.9670 (mtpp) cc_final: 0.9424 (mtmm) REVERT: E 84 ASN cc_start: 0.9325 (t0) cc_final: 0.9063 (m110) REVERT: K 4 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7658 (tm130) REVERT: K 11 GLU cc_start: 0.8668 (pm20) cc_final: 0.8335 (mp0) REVERT: K 14 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7282 (tpm170) REVERT: K 64 LYS cc_start: 0.9311 (ttpt) cc_final: 0.8988 (ttpt) REVERT: K 86 ARG cc_start: 0.9225 (mmp80) cc_final: 0.8955 (mmp80) REVERT: O 24 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7787 (ttmm) REVERT: O 45 ARG cc_start: 0.8367 (tpp80) cc_final: 0.7813 (tpp80) REVERT: O 64 LYS cc_start: 0.9346 (ttpp) cc_final: 0.9097 (ttpp) REVERT: O 66 LYS cc_start: 0.9247 (tppt) cc_final: 0.8583 (mmmt) REVERT: O 113 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8690 (pm20) REVERT: O 116 LEU cc_start: 0.9344 (tt) cc_final: 0.9069 (tm) REVERT: L 24 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8716 (mppt) REVERT: L 27 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8026 (tm-30) REVERT: L 63 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8508 (p) REVERT: L 77 ASN cc_start: 0.8290 (t0) cc_final: 0.8000 (t0) REVERT: L 85 GLU cc_start: 0.7802 (tp30) cc_final: 0.7478 (tp30) REVERT: L 103 LYS cc_start: 0.8435 (tppp) cc_final: 0.8110 (tppt) REVERT: J 40 ARG cc_start: 0.9107 (tmm-80) cc_final: 0.8876 (ttp80) REVERT: J 63 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8821 (p) REVERT: J 82 ASP cc_start: 0.8863 (m-30) cc_final: 0.8495 (m-30) REVERT: J 85 GLU cc_start: 0.8018 (mp0) cc_final: 0.7648 (mp0) REVERT: N 77 ASN cc_start: 0.8762 (t0) cc_final: 0.8398 (t0) REVERT: N 81 GLU cc_start: 0.8997 (pt0) cc_final: 0.8622 (pm20) REVERT: N 85 GLU cc_start: 0.8001 (tp30) cc_final: 0.7539 (tp30) REVERT: N 103 LYS cc_start: 0.8745 (tppp) cc_final: 0.8365 (tppt) outliers start: 39 outliers final: 22 residues processed: 318 average time/residue: 0.6520 time to fit residues: 231.1924 Evaluate side-chains 319 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 113 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: [202, 18, 217, 91, 153, 125, 32, 174, 141, 134, 171] chunk 202 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 174 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.073567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.049385 restraints weight = 55732.710| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.68 r_work: 0.2661 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19686 Z= 0.129 Angle : 0.730 13.101 26745 Z= 0.360 Chirality : 0.043 0.187 2943 Planarity : 0.004 0.059 3357 Dihedral : 4.427 18.962 2859 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.71 % Allowed : 20.82 % Favored : 77.48 % 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: 0.28 (0.17), residues: 2403 helix: 1.81 (0.37), residues: 198 sheet: 0.72 (0.18), residues: 810 loop : -0.34 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 45 TYR 0.021 0.001 TYR A 145 PHE 0.013 0.001 PHE L 10 TRP 0.014 0.001 TRP A 100 HIS 0.004 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (19644) covalent geometry : angle 0.72936 / 0.36 (26652) SS BOND : bond 0.00237 / 0.16 ( 33) SS BOND : angle 0.72499 / 0.48 ( 66) hydrogen bonds : bond 0.02966 / 1.98 ( 632) hydrogen bonds : angle 5.16138 / 3.64 ( 1596) link_NAG-ASN : bond 0.00105 / 0.06 ( 9) link_NAG-ASN : angle 1.02704 / 0.65 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6825.49 seconds wall clock time: 116 minutes 58.70 seconds (7018.70 seconds total)