Starting phenix.real_space_refine on Mon Oct 26 06:31:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyh_46044/10_2026/9cyh_46044.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyh_46044/10_2026/9cyh_46044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cyh_46044/10_2026/9cyh_46044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyh_46044/10_2026/9cyh_46044.map" model { file = "/net/cci-nas-00/data/ceres_data/9cyh_46044/10_2026/9cyh_46044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyh_46044/10_2026/9cyh_46044.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 148 5.16 5 C 12240 2.51 5 N 3320 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 19488 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3016 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 371} Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "I" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, F, G, H, J, K, L, O, Q, S, P, R, T Time building chain proxies: 4.12, per 1000 atoms: 0.21 Number of scatterers: 19488 At special positions: 0 Unit cell: (137.025, 137.025, 91.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 148 16.00 O 3776 8.00 N 3320 7.00 C 12240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 424 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 229 " distance=2.03 Simple disulfide: pdb=" SG CYS B 231 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 231 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 420 " distance=2.03 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 231 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 424 " - pdb=" SG CYS D 447 " 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 BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG M 1 " - " ASN A 144 " " NAG N 1 " - " ASN A 284 " " NAG O 1 " - " ASN B 144 " " NAG P 1 " - " ASN B 284 " " NAG Q 1 " - " ASN C 144 " " NAG R 1 " - " ASN C 284 " " NAG S 1 " - " ASN D 144 " " NAG T 1 " - " ASN D 284 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 680.1 milliseconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 52 sheets defined 1.6% alpha, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'D' and resid 99 through 104 Processing sheet with id=AA1, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.599A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N CYS H 92 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU H 4 " --> pdb=" O GLN H 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.599A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.738A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.345A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 98 removed outlier: 5.414A pdb=" N LYS A 94 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N CYS A 447 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 113 through 122 removed outlier: 4.638A pdb=" N LEU A 113 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ALA A 136 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE A 115 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS A 134 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU A 117 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 132 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 156 " --> pdb=" O HIS A 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.688A pdb=" N SER A 178 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A 212 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR A 206 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TYR A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AB2, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.589A pdb=" N LYS A 263 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 257 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.534A pdb=" N THR A 268 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N LEU A 316 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG A 292 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU A 276 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 352 through 356 removed outlier: 7.771A pdb=" N MET A 375 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL A 401 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET A 377 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL A 399 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 379 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 58 through 59 removed outlier: 6.599A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP E 35A" --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N CYS E 92 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU E 4 " --> pdb=" O GLN E 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 58 through 59 removed outlier: 6.599A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP E 35A" --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.737A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.343A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AC2, first strand: chain 'B' and resid 92 through 98 removed outlier: 5.415A pdb=" N LYS B 94 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N CYS B 447 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 113 through 122 removed outlier: 4.639A pdb=" N LEU B 113 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA B 136 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE B 115 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS B 134 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU B 117 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU B 132 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 156 " --> pdb=" O HIS B 173 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 178 through 183 removed outlier: 3.688A pdb=" N SER B 178 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 212 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR B 206 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYR B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AC6, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.588A pdb=" N LYS B 263 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B 257 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 268 through 269 removed outlier: 6.535A pdb=" N THR B 268 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N LEU B 316 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 292 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU B 276 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 352 through 356 removed outlier: 7.772A pdb=" N MET B 375 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL B 401 " --> pdb=" O MET B 375 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET B 377 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL B 399 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 379 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 58 through 59 removed outlier: 6.600A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP F 35A" --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N CYS F 92 " --> pdb=" O GLY F 104 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LEU F 4 " --> pdb=" O GLN F 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 58 through 59 removed outlier: 6.600A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP F 35A" --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AD3, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.737A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.344A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD6, first strand: chain 'C' and resid 92 through 98 removed outlier: 5.415A pdb=" N LYS C 94 " --> pdb=" O CYS C 447 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N CYS C 447 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 113 through 122 removed outlier: 4.638A pdb=" N LEU C 113 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA C 136 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE C 115 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS C 134 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 132 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 156 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 178 through 183 removed outlier: 3.689A pdb=" N SER C 178 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR C 206 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR C 210 " --> pdb=" O TYR C 206 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AE1, first strand: chain 'C' and resid 223 through 224 removed outlier: 3.587A pdb=" N LYS C 263 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG C 257 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 268 through 269 removed outlier: 6.534A pdb=" N THR C 268 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N LEU C 316 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG C 292 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU C 276 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 352 through 356 removed outlier: 7.769A pdb=" N MET C 375 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL C 401 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET C 377 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL C 399 " --> pdb=" O MET C 377 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 379 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 58 through 59 removed outlier: 6.599A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N CYS G 92 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU G 4 " --> pdb=" O GLN G 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 58 through 59 removed outlier: 6.599A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.738A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.343A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AF1, first strand: chain 'D' and resid 92 through 98 removed outlier: 5.415A pdb=" N LYS D 94 " --> pdb=" O CYS D 447 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N CYS D 447 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 113 through 122 removed outlier: 4.638A pdb=" N LEU D 113 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA D 136 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE D 115 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS D 134 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU D 117 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU D 132 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU D 156 " --> pdb=" O HIS D 173 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 178 through 183 removed outlier: 3.686A pdb=" N SER D 178 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP D 212 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR D 206 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TYR D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AF5, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.591A pdb=" N LYS D 263 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG D 257 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 268 through 269 removed outlier: 6.535A pdb=" N THR D 268 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N LEU D 316 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG D 292 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU D 276 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 352 through 356 removed outlier: 7.772A pdb=" N MET D 375 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL D 401 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET D 377 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL D 399 " --> pdb=" O MET D 377 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU D 379 " --> pdb=" O SER D 397 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1740 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: 5.16 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6256 1.35 - 1.47: 5230 1.47 - 1.59: 8266 1.59 - 1.71: 0 1.71 - 1.83: 212 Bond restraints: 19964 Sorted by residual: bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.53e+00 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" C GLN L 79 " pdb=" N PRO L 80 " ideal model delta sigma weight residual 1.334 1.374 -0.040 1.51e-02 4.39e+03 6.96e+00 ... (remaining 19959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 25694 1.92 - 3.85: 1062 3.85 - 5.77: 244 5.77 - 7.69: 36 7.69 - 9.61: 8 Bond angle restraints: 27044 Sorted by residual: angle pdb=" CA ILE H 82A" pdb=" CB ILE H 82A" pdb=" CG1 ILE H 82A" ideal model delta sigma weight residual 110.40 116.09 -5.69 1.70e+00 3.46e-01 1.12e+01 angle pdb=" CA ILE G 82A" pdb=" CB ILE G 82A" pdb=" CG1 ILE G 82A" ideal model delta sigma weight residual 110.40 116.09 -5.69 1.70e+00 3.46e-01 1.12e+01 angle pdb=" CA ILE F 82A" pdb=" CB ILE F 82A" pdb=" CG1 ILE F 82A" ideal model delta sigma weight residual 110.40 116.03 -5.63 1.70e+00 3.46e-01 1.10e+01 angle pdb=" CA ILE E 82A" pdb=" CB ILE E 82A" pdb=" CG1 ILE E 82A" ideal model delta sigma weight residual 110.40 116.03 -5.63 1.70e+00 3.46e-01 1.10e+01 angle pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 111.30 117.96 -6.66 2.30e+00 1.89e-01 8.38e+00 ... (remaining 27039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 10518 17.64 - 35.28: 1106 35.28 - 52.93: 280 52.93 - 70.57: 68 70.57 - 88.21: 36 Dihedral angle restraints: 12008 sinusoidal: 4948 harmonic: 7060 Sorted by residual: dihedral pdb=" CD ARG J 24 " pdb=" NE ARG J 24 " pdb=" CZ ARG J 24 " pdb=" NH1 ARG J 24 " ideal model delta sinusoidal sigma weight residual 0.00 -65.54 65.54 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CD ARG K 24 " pdb=" NE ARG K 24 " pdb=" CZ ARG K 24 " pdb=" NH1 ARG K 24 " ideal model delta sinusoidal sigma weight residual 0.00 -65.51 65.51 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CD ARG I 24 " pdb=" NE ARG I 24 " pdb=" CZ ARG I 24 " pdb=" NH1 ARG I 24 " ideal model delta sinusoidal sigma weight residual 0.00 -65.44 65.44 1 1.00e+01 1.00e-02 5.61e+01 ... (remaining 12005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2031 0.051 - 0.101: 664 0.101 - 0.151: 193 0.151 - 0.202: 16 0.202 - 0.252: 4 Chirality restraints: 2908 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A 284 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN B 284 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 284 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2905 not shown) Planarity restraints: 3464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 24 " -0.846 9.50e-02 1.11e+02 3.80e-01 9.62e+01 pdb=" NE ARG J 24 " 0.070 2.00e-02 2.50e+03 pdb=" CZ ARG J 24 " -0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG J 24 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG J 24 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 150 " -0.848 9.50e-02 1.11e+02 3.81e-01 9.60e+01 pdb=" NE ARG B 150 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG B 150 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG B 150 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 150 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 150 " -0.848 9.50e-02 1.11e+02 3.81e-01 9.60e+01 pdb=" NE ARG C 150 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG C 150 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG C 150 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 150 " -0.006 2.00e-02 2.50e+03 ... (remaining 3461 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4346 2.79 - 3.32: 17228 3.32 - 3.84: 34316 3.84 - 4.37: 42148 4.37 - 4.90: 73628 Nonbonded interactions: 171666 Sorted by model distance: nonbonded pdb=" O GLY D 346 " pdb="CA CA D 501 " model vdw 2.262 2.510 nonbonded pdb=" O GLY B 346 " pdb="CA CA B 501 " model vdw 2.263 2.510 nonbonded pdb=" O GLY A 346 " pdb="CA CA A 501 " model vdw 2.263 2.510 nonbonded pdb=" O GLY C 346 " pdb="CA CA C 501 " model vdw 2.263 2.510 nonbonded pdb=" OD2 ASP C 324 " pdb="CA CA C 501 " model vdw 2.268 2.510 ... (remaining 171661 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 12.500 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.800 Find NCS groups from input model: 0.510 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: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20020 Z= 0.230 Angle : 0.944 10.117 27172 Z= 0.471 Chirality : 0.053 0.252 2908 Planarity : 0.025 0.381 3456 Dihedral : 16.029 88.208 7440 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.77 % Allowed : 17.46 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.92 (0.15), residues: 2476 helix: None (None), residues: 0 sheet: -0.71 (0.16), residues: 920 loop : -1.69 (0.13), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.006 ARG J 24 TYR 0.025 0.002 TYR B 237 PHE 0.022 0.002 PHE A 130 TRP 0.013 0.001 TRP C 177 HIS 0.013 0.002 HIS G 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (19964) covalent geometry : angle 0.91927 / 0.47 (27044) SS BOND : bond 0.00246 / 0.16 ( 40) SS BOND : angle 1.55666 / 1.09 ( 80) hydrogen bonds : bond 0.25967 / 17.19 ( 616) hydrogen bonds : angle 10.57105 / 7.43 ( 1740) link_BETA1-4 : bond 0.00114 / 0.07 ( 8) link_BETA1-4 : angle 3.01023 / 2.61 ( 24) link_NAG-ASN : bond 0.00708 / 0.35 ( 8) link_NAG-ASN : angle 6.37134 / 4.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 516 time to evaluate : 0.747 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 528 average time/residue: 0.5384 time to fit residues: 324.7661 Evaluate side-chains 404 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 396 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 16 GLN H 40 HIS A 183 HIS A 294 ASN A 431 HIS E 16 GLN E 40 HIS B 183 HIS B 294 ASN B 431 HIS F 16 GLN F 40 HIS C 183 HIS C 294 ASN C 431 HIS G 16 GLN G 40 HIS D 183 HIS D 294 ASN D 431 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.141080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.104284 restraints weight = 25086.686| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.41 r_work: 0.3330 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20020 Z= 0.193 Angle : 0.707 8.585 27172 Z= 0.364 Chirality : 0.048 0.170 2908 Planarity : 0.005 0.043 3456 Dihedral : 7.214 59.066 3088 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.19 % Favored : 96.65 % Rotamer: Outliers : 5.13 % Allowed : 19.00 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.37 (0.16), residues: 992 loop : -1.42 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 81 TYR 0.015 0.002 TYR F 100D PHE 0.018 0.002 PHE F 78 TRP 0.013 0.001 TRP A 177 HIS 0.007 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (19964) covalent geometry : angle 0.68214 / 0.36 (27044) SS BOND : bond 0.00464 / 0.30 ( 40) SS BOND : angle 1.39143 / 0.90 ( 80) hydrogen bonds : bond 0.04739 / 3.14 ( 616) hydrogen bonds : angle 6.97934 / 4.91 ( 1740) link_BETA1-4 : bond 0.00277 / 0.17 ( 8) link_BETA1-4 : angle 2.48311 / 2.10 ( 24) link_NAG-ASN : bond 0.00692 / 0.39 ( 8) link_NAG-ASN : angle 5.44083 / 3.86 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 425 time to evaluate : 0.719 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: H 13 LYS cc_start: 0.8698 (tttp) cc_final: 0.8401 (mmpt) REVERT: H 81 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.7912 (mmm-85) REVERT: H 102 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8118 (m) REVERT: H 105 GLN cc_start: 0.7177 (pm20) cc_final: 0.6754 (pm20) REVERT: L 24 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7501 (mmm-85) REVERT: E 13 LYS cc_start: 0.8697 (tttp) cc_final: 0.8400 (mmpt) REVERT: E 81 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.7905 (mmm-85) REVERT: E 100 MET cc_start: 0.7626 (mtt) cc_final: 0.7426 (mtt) REVERT: E 102 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8120 (m) REVERT: E 105 GLN cc_start: 0.7190 (pm20) cc_final: 0.6765 (pm20) REVERT: I 24 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7496 (mmm-85) REVERT: F 13 LYS cc_start: 0.8698 (tttp) cc_final: 0.8401 (mmpt) REVERT: F 81 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.7908 (mmm-85) REVERT: F 102 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8113 (m) REVERT: F 105 GLN cc_start: 0.7180 (pm20) cc_final: 0.6755 (pm20) REVERT: J 24 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7506 (mmm-85) REVERT: G 13 LYS cc_start: 0.8699 (tttp) cc_final: 0.8402 (mmpt) REVERT: G 81 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.7907 (mmm-85) REVERT: G 102 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8118 (m) REVERT: G 105 GLN cc_start: 0.7183 (pm20) cc_final: 0.6760 (pm20) REVERT: K 24 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7497 (mmm-85) REVERT: D 377 MET cc_start: 0.8206 (tpp) cc_final: 0.7923 (tpp) outliers start: 106 outliers final: 53 residues processed: 469 average time/residue: 0.5177 time to fit residues: 278.2187 Evaluate side-chains 465 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 408 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [150, 83, 3, 210, 179, 121, 226, 100, 158, 72, 155] chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.138705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.101535 restraints weight = 25546.215| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.41 r_work: 0.3283 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20020 Z= 0.242 Angle : 0.684 7.437 27172 Z= 0.357 Chirality : 0.049 0.174 2908 Planarity : 0.005 0.041 3456 Dihedral : 6.705 59.501 3080 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 4.21 % Allowed : 21.32 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.30 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.32 (0.17), residues: 948 loop : -1.24 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 81 TYR 0.012 0.002 TYR H 100D PHE 0.020 0.002 PHE G 78 TRP 0.014 0.001 TRP C 177 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (19964) covalent geometry : angle 0.66658 / 0.35 (27044) SS BOND : bond 0.00449 / 0.30 ( 40) SS BOND : angle 1.30044 / 0.87 ( 80) hydrogen bonds : bond 0.04359 / 2.89 ( 616) hydrogen bonds : angle 6.51403 / 4.58 ( 1740) link_BETA1-4 : bond 0.00235 / 0.14 ( 8) link_BETA1-4 : angle 2.30589 / 1.90 ( 24) link_NAG-ASN : bond 0.00514 / 0.30 ( 8) link_NAG-ASN : angle 4.27780 / 2.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 409 time to evaluate : 0.614 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: H 13 LYS cc_start: 0.8697 (tttp) cc_final: 0.8387 (mmpt) REVERT: H 66 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.7999 (ttm170) REVERT: H 81 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8308 (mmm-85) REVERT: H 102 VAL cc_start: 0.8385 (p) cc_final: 0.8179 (m) REVERT: H 105 GLN cc_start: 0.7521 (pm20) cc_final: 0.7011 (pm20) REVERT: L 24 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7562 (mmm-85) REVERT: L 79 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6831 (mm110) REVERT: A 138 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: A 377 MET cc_start: 0.8298 (tpp) cc_final: 0.8052 (tpp) REVERT: A 416 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8251 (mttp) REVERT: E 13 LYS cc_start: 0.8696 (tttp) cc_final: 0.8388 (mmpt) REVERT: E 66 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.7995 (ttm170) REVERT: E 81 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8307 (mmm-85) REVERT: E 96 ASP cc_start: 0.8312 (t70) cc_final: 0.8029 (t70) REVERT: E 102 VAL cc_start: 0.8374 (p) cc_final: 0.8159 (m) REVERT: E 105 GLN cc_start: 0.7520 (pm20) cc_final: 0.7011 (pm20) REVERT: I 24 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7569 (mmm-85) REVERT: I 79 GLN cc_start: 0.7100 (mm-40) cc_final: 0.6799 (mm110) REVERT: B 138 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: B 377 MET cc_start: 0.8284 (tpp) cc_final: 0.8039 (tpp) REVERT: B 416 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8254 (mttp) REVERT: F 13 LYS cc_start: 0.8698 (tttp) cc_final: 0.8390 (mmpt) REVERT: F 66 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.7992 (ttm170) REVERT: F 81 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8306 (mmm-85) REVERT: F 96 ASP cc_start: 0.8317 (t70) cc_final: 0.8017 (t70) REVERT: F 102 VAL cc_start: 0.8407 (p) cc_final: 0.8198 (m) REVERT: F 105 GLN cc_start: 0.7502 (pm20) cc_final: 0.6992 (pm20) REVERT: J 24 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7564 (mmm-85) REVERT: J 79 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6800 (mm110) REVERT: C 138 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: C 377 MET cc_start: 0.8276 (tpp) cc_final: 0.8029 (tpp) REVERT: C 416 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8236 (mttp) REVERT: G 13 LYS cc_start: 0.8696 (tttp) cc_final: 0.8387 (mmpt) REVERT: G 66 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.7996 (ttm170) REVERT: G 81 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8307 (mmm-85) REVERT: G 96 ASP cc_start: 0.8315 (t70) cc_final: 0.8027 (t70) REVERT: G 102 VAL cc_start: 0.8386 (p) cc_final: 0.8179 (m) REVERT: G 105 GLN cc_start: 0.7504 (pm20) cc_final: 0.6996 (pm20) REVERT: K 24 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7561 (mmm-85) REVERT: K 79 GLN cc_start: 0.7114 (mm-40) cc_final: 0.6833 (mm110) REVERT: D 138 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: D 377 MET cc_start: 0.8309 (tpp) cc_final: 0.8092 (tpp) REVERT: D 416 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8237 (mttp) outliers start: 87 outliers final: 66 residues processed: 442 average time/residue: 0.5437 time to fit residues: 273.5928 Evaluate side-chains 469 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 395 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [178, 217, 172, 186, 189, 221, 195, 207, 151, 100, 241] chunk 178 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 172 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 195 optimal weight: 0.0670 chunk 207 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.141990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106062 restraints weight = 25385.266| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.38 r_work: 0.3359 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20020 Z= 0.136 Angle : 0.618 6.833 27172 Z= 0.321 Chirality : 0.046 0.150 2908 Planarity : 0.004 0.040 3456 Dihedral : 6.186 59.219 3080 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.39 % Favored : 96.45 % Rotamer: Outliers : 4.69 % Allowed : 21.08 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.06 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.06 (0.17), residues: 976 loop : -1.18 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 56 TYR 0.012 0.001 TYR F 100D PHE 0.019 0.002 PHE H 78 TRP 0.011 0.001 TRP A 177 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (19964) covalent geometry : angle 0.60401 / 0.32 (27044) SS BOND : bond 0.00317 / 0.21 ( 40) SS BOND : angle 0.87650 / 0.58 ( 80) hydrogen bonds : bond 0.03615 / 2.40 ( 616) hydrogen bonds : angle 6.10434 / 4.29 ( 1740) link_BETA1-4 : bond 0.00279 / 0.15 ( 8) link_BETA1-4 : angle 2.32656 / 1.93 ( 24) link_NAG-ASN : bond 0.00552 / 0.32 ( 8) link_NAG-ASN : angle 3.60760 / 2.14 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 416 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 ARG cc_start: 0.8354 (ttp-110) cc_final: 0.7989 (ttm170) REVERT: H 81 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8256 (mmm-85) REVERT: H 102 VAL cc_start: 0.8425 (p) cc_final: 0.8186 (m) REVERT: H 105 GLN cc_start: 0.7843 (pm20) cc_final: 0.7300 (pm20) REVERT: L 24 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7638 (mmm-85) REVERT: L 79 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6762 (mm110) REVERT: A 416 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8107 (mttp) REVERT: E 66 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.8000 (ttm170) REVERT: E 81 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.8259 (mmm-85) REVERT: E 96 ASP cc_start: 0.8332 (t70) cc_final: 0.8007 (t70) REVERT: E 102 VAL cc_start: 0.8420 (p) cc_final: 0.8219 (m) REVERT: E 105 GLN cc_start: 0.7828 (pm20) cc_final: 0.7264 (pm20) REVERT: I 24 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7636 (mmm-85) REVERT: I 79 GLN cc_start: 0.7166 (mm-40) cc_final: 0.6825 (mm110) REVERT: B 416 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8110 (mttp) REVERT: F 66 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.7992 (ttm170) REVERT: F 81 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8256 (mmm-85) REVERT: F 102 VAL cc_start: 0.8433 (p) cc_final: 0.8194 (m) REVERT: F 105 GLN cc_start: 0.7845 (pm20) cc_final: 0.7299 (pm20) REVERT: J 24 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7636 (mmm-85) REVERT: J 79 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6876 (mm110) REVERT: C 416 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8105 (mttp) REVERT: G 66 ARG cc_start: 0.8354 (ttp-110) cc_final: 0.7988 (ttm170) REVERT: G 81 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8259 (mmm-85) REVERT: G 102 VAL cc_start: 0.8423 (p) cc_final: 0.8185 (m) REVERT: G 105 GLN cc_start: 0.7820 (pm20) cc_final: 0.7260 (pm20) REVERT: K 24 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7637 (mmm-85) REVERT: K 79 GLN cc_start: 0.7157 (mm-40) cc_final: 0.6691 (mm110) REVERT: D 416 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8106 (mttp) outliers start: 97 outliers final: 50 residues processed: 464 average time/residue: 0.5143 time to fit residues: 274.6631 Evaluate side-chains 453 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 399 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [53, 56, 102, 201, 76, 80, 20, 93, 104, 153, 213] chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104351 restraints weight = 25313.107| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.37 r_work: 0.3332 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20020 Z= 0.185 Angle : 0.636 8.063 27172 Z= 0.328 Chirality : 0.046 0.149 2908 Planarity : 0.005 0.044 3456 Dihedral : 5.898 59.296 3080 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 4.74 % Allowed : 21.95 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.99 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: 0.01 (0.17), residues: 976 loop : -1.15 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 56 TYR 0.012 0.001 TYR F 100D PHE 0.019 0.002 PHE G 78 TRP 0.011 0.001 TRP C 177 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (19964) covalent geometry : angle 0.62234 / 0.33 (27044) SS BOND : bond 0.00368 / 0.25 ( 40) SS BOND : angle 1.04360 / 0.70 ( 80) hydrogen bonds : bond 0.03647 / 2.42 ( 616) hydrogen bonds : angle 6.03257 / 4.24 ( 1740) link_BETA1-4 : bond 0.00257 / 0.14 ( 8) link_BETA1-4 : angle 2.33105 / 1.93 ( 24) link_NAG-ASN : bond 0.00518 / 0.31 ( 8) link_NAG-ASN : angle 3.47574 / 1.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 397 time to evaluate : 0.579 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: H 13 LYS cc_start: 0.8725 (tptp) cc_final: 0.8318 (mmpt) REVERT: H 66 ARG cc_start: 0.8388 (ttp-110) cc_final: 0.8022 (ttm170) REVERT: H 81 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8171 (mmm-85) REVERT: H 102 VAL cc_start: 0.8482 (p) cc_final: 0.8229 (m) REVERT: H 105 GLN cc_start: 0.7988 (pm20) cc_final: 0.7426 (pm20) REVERT: L 24 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7692 (mmm-85) REVERT: L 79 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6731 (mm110) REVERT: A 138 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: A 416 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8138 (mttp) REVERT: E 13 LYS cc_start: 0.8723 (tptp) cc_final: 0.8316 (mmpt) REVERT: E 66 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8033 (ttm170) REVERT: E 81 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8167 (mmm-85) REVERT: E 96 ASP cc_start: 0.8396 (t0) cc_final: 0.8089 (t70) REVERT: E 102 VAL cc_start: 0.8457 (p) cc_final: 0.8233 (m) REVERT: E 105 GLN cc_start: 0.7972 (pm20) cc_final: 0.7409 (pm20) REVERT: I 24 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7693 (mmm-85) REVERT: I 79 GLN cc_start: 0.7151 (mm-40) cc_final: 0.6781 (mm110) REVERT: B 138 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: B 416 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8143 (mttp) REVERT: F 13 LYS cc_start: 0.8723 (tptp) cc_final: 0.8315 (mmpt) REVERT: F 66 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8030 (ttm170) REVERT: F 81 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8170 (mmm-85) REVERT: F 96 ASP cc_start: 0.8436 (t70) cc_final: 0.8141 (t70) REVERT: F 102 VAL cc_start: 0.8498 (p) cc_final: 0.8245 (m) REVERT: F 105 GLN cc_start: 0.7994 (pm20) cc_final: 0.7431 (pm20) REVERT: J 24 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7695 (mmm-85) REVERT: J 79 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6713 (mm110) REVERT: C 138 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: C 416 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8138 (mttp) REVERT: G 13 LYS cc_start: 0.8723 (tptp) cc_final: 0.8315 (mmpt) REVERT: G 66 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.8019 (ttm170) REVERT: G 81 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8170 (mmm-85) REVERT: G 96 ASP cc_start: 0.8436 (t70) cc_final: 0.8178 (t70) REVERT: G 102 VAL cc_start: 0.8493 (p) cc_final: 0.8241 (m) REVERT: G 105 GLN cc_start: 0.7994 (pm20) cc_final: 0.7430 (pm20) REVERT: K 24 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7701 (mmm-85) REVERT: K 79 GLN cc_start: 0.7121 (mm-40) cc_final: 0.6794 (mm110) REVERT: D 138 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: D 416 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8134 (mttp) outliers start: 98 outliers final: 64 residues processed: 445 average time/residue: 0.5177 time to fit residues: 263.7208 Evaluate side-chains 447 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 375 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [110, 46, 174, 145, 205, 60, 133, 49, 52, 69, 218] chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 218 optimal weight: 0.3980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.137818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101239 restraints weight = 25342.347| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.35 r_work: 0.3290 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20020 Z= 0.280 Angle : 0.698 8.716 27172 Z= 0.363 Chirality : 0.048 0.155 2908 Planarity : 0.005 0.056 3456 Dihedral : 6.026 58.914 3080 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.76 % Favored : 96.08 % Rotamer: Outliers : 4.98 % Allowed : 21.86 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.18 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.17 (0.16), residues: 1032 loop : -1.26 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 56 TYR 0.012 0.002 TYR B 383 PHE 0.019 0.002 PHE G 78 TRP 0.012 0.001 TRP A 177 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.28 (19964) covalent geometry : angle 0.68455 / 0.36 (27044) SS BOND : bond 0.00431 / 0.30 ( 40) SS BOND : angle 1.35107 / 0.91 ( 80) hydrogen bonds : bond 0.03908 / 2.59 ( 616) hydrogen bonds : angle 6.19464 / 4.36 ( 1740) link_BETA1-4 : bond 0.00243 / 0.14 ( 8) link_BETA1-4 : angle 2.27255 / 1.85 ( 24) link_NAG-ASN : bond 0.00458 / 0.27 ( 8) link_NAG-ASN : angle 3.57995 / 1.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 402 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.7975 (ttm170) REVERT: H 81 ARG cc_start: 0.8553 (mmm-85) cc_final: 0.8197 (mmm-85) REVERT: H 105 GLN cc_start: 0.8093 (pm20) cc_final: 0.7629 (pm20) REVERT: L 24 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7637 (mmm-85) REVERT: L 79 GLN cc_start: 0.7058 (mm-40) cc_final: 0.6841 (mm110) REVERT: A 138 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: A 416 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8149 (mttp) REVERT: A 449 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8193 (mmt) REVERT: E 66 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.7986 (ttm170) REVERT: E 81 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8182 (mmm-85) REVERT: E 96 ASP cc_start: 0.8390 (t0) cc_final: 0.8150 (t70) REVERT: E 105 GLN cc_start: 0.8093 (pm20) cc_final: 0.7631 (pm20) REVERT: I 24 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7641 (mmm-85) REVERT: I 79 GLN cc_start: 0.7120 (mm-40) cc_final: 0.6815 (mm110) REVERT: B 138 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: B 416 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8154 (mttp) REVERT: B 449 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8198 (mmt) REVERT: F 66 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.7981 (ttm170) REVERT: F 81 ARG cc_start: 0.8553 (mmm-85) cc_final: 0.8197 (mmm-85) REVERT: F 105 GLN cc_start: 0.8106 (pm20) cc_final: 0.7641 (pm20) REVERT: J 24 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7645 (mmm-85) REVERT: J 79 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6688 (mm110) REVERT: C 138 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: C 416 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8156 (mttp) REVERT: C 449 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8203 (mmt) REVERT: G 66 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.7974 (ttm170) REVERT: G 81 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8200 (mmm-85) REVERT: G 105 GLN cc_start: 0.8104 (pm20) cc_final: 0.7639 (pm20) REVERT: K 24 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7638 (mmm-85) REVERT: K 79 GLN cc_start: 0.7027 (mm-40) cc_final: 0.6750 (mm110) REVERT: D 138 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: D 416 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8150 (mttp) REVERT: D 449 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8200 (mmt) outliers start: 103 outliers final: 60 residues processed: 442 average time/residue: 0.5223 time to fit residues: 265.8332 Evaluate side-chains 466 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 394 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [139, 36, 219, 119, 234, 229, 33, 123, 85, 54, 70] chunk 139 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 219 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 60 ASN E 60 ASN F 60 ASN G 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.141029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104586 restraints weight = 25450.970| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.39 r_work: 0.3340 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20020 Z= 0.152 Angle : 0.636 10.400 27172 Z= 0.327 Chirality : 0.046 0.146 2908 Planarity : 0.005 0.065 3456 Dihedral : 5.771 58.721 3080 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.61 % Rotamer: Outliers : 3.24 % Allowed : 24.81 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.92 (0.17), residues: 2476 helix: None (None), residues: 0 sheet: 0.01 (0.17), residues: 988 loop : -1.05 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 56 TYR 0.012 0.001 TYR H 100D PHE 0.018 0.002 PHE F 78 TRP 0.013 0.001 TRP A 177 HIS 0.007 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (19964) covalent geometry : angle 0.62416 / 0.32 (27044) SS BOND : bond 0.00320 / 0.22 ( 40) SS BOND : angle 0.89948 / 0.60 ( 80) hydrogen bonds : bond 0.03419 / 2.27 ( 616) hydrogen bonds : angle 6.00718 / 4.22 ( 1740) link_BETA1-4 : bond 0.00280 / 0.16 ( 8) link_BETA1-4 : angle 2.26425 / 1.86 ( 24) link_NAG-ASN : bond 0.00523 / 0.31 ( 8) link_NAG-ASN : angle 3.38337 / 1.86 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 392 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.8745 (tppt) cc_final: 0.8427 (mmpt) REVERT: H 66 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.8122 (ttp-110) REVERT: H 81 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8162 (mmm-85) REVERT: H 105 GLN cc_start: 0.8261 (pm20) cc_final: 0.7847 (pm20) REVERT: L 24 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7700 (mmm-85) REVERT: L 45 LYS cc_start: 0.7857 (tttm) cc_final: 0.7528 (pttp) REVERT: L 79 GLN cc_start: 0.7128 (mm-40) cc_final: 0.6834 (mm110) REVERT: A 416 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8025 (mttp) REVERT: E 13 LYS cc_start: 0.8750 (tppt) cc_final: 0.8430 (mmpt) REVERT: E 66 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.8138 (ttp-110) REVERT: E 81 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8169 (mmm-85) REVERT: E 102 VAL cc_start: 0.8529 (p) cc_final: 0.8280 (m) REVERT: E 105 GLN cc_start: 0.8283 (pm20) cc_final: 0.7868 (pm20) REVERT: I 24 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7704 (mmm-85) REVERT: I 79 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6804 (mm110) REVERT: B 138 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: B 416 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8030 (mttp) REVERT: F 13 LYS cc_start: 0.8751 (tppt) cc_final: 0.8430 (mmpt) REVERT: F 66 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.8125 (ttp-110) REVERT: F 81 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8174 (mmm-85) REVERT: F 105 GLN cc_start: 0.8264 (pm20) cc_final: 0.7848 (pm20) REVERT: J 24 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7690 (mmm-85) REVERT: J 45 LYS cc_start: 0.7883 (tttm) cc_final: 0.7549 (pttp) REVERT: J 79 GLN cc_start: 0.7125 (mm-40) cc_final: 0.6825 (mm110) REVERT: C 416 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8024 (mttp) REVERT: G 13 LYS cc_start: 0.8745 (tppt) cc_final: 0.8427 (mmpt) REVERT: G 66 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.8123 (ttp-110) REVERT: G 81 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: G 105 GLN cc_start: 0.8270 (pm20) cc_final: 0.7853 (pm20) REVERT: K 24 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7701 (mmm-85) REVERT: K 45 LYS cc_start: 0.7845 (tttm) cc_final: 0.7514 (pttp) REVERT: K 79 GLN cc_start: 0.7192 (mm-40) cc_final: 0.6731 (mm110) REVERT: D 416 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8023 (mttp) outliers start: 67 outliers final: 42 residues processed: 429 average time/residue: 0.5261 time to fit residues: 259.5545 Evaluate side-chains 401 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 354 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [20, 149, 195, 228, 173, 34, 38, 100, 72, 76, 143] chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 195 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.139993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103879 restraints weight = 25509.400| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.36 r_work: 0.3325 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20020 Z= 0.185 Angle : 0.655 10.807 27172 Z= 0.338 Chirality : 0.047 0.148 2908 Planarity : 0.005 0.074 3456 Dihedral : 5.749 59.020 3080 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.12 % Rotamer: Outliers : 4.30 % Allowed : 24.37 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.95 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.00 (0.17), residues: 988 loop : -1.08 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 56 TYR 0.013 0.002 TYR B 237 PHE 0.019 0.002 PHE E 78 TRP 0.012 0.001 TRP A 177 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (19964) covalent geometry : angle 0.64328 / 0.34 (27044) SS BOND : bond 0.00342 / 0.24 ( 40) SS BOND : angle 1.07014 / 0.72 ( 80) hydrogen bonds : bond 0.03527 / 2.34 ( 616) hydrogen bonds : angle 5.95826 / 4.19 ( 1740) link_BETA1-4 : bond 0.00273 / 0.16 ( 8) link_BETA1-4 : angle 2.23242 / 1.82 ( 24) link_NAG-ASN : bond 0.00513 / 0.30 ( 8) link_NAG-ASN : angle 3.36139 / 1.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 355 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6630 (mp0) cc_final: 0.6401 (mp0) REVERT: H 66 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.7944 (ttm170) REVERT: H 81 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8152 (mmm-85) REVERT: H 102 VAL cc_start: 0.8471 (p) cc_final: 0.8221 (m) REVERT: H 105 GLN cc_start: 0.8284 (pm20) cc_final: 0.8065 (pm20) REVERT: L 24 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7670 (mmm-85) REVERT: L 45 LYS cc_start: 0.7755 (tttm) cc_final: 0.7414 (pttp) REVERT: L 79 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6731 (mm110) REVERT: A 416 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8030 (mttp) REVERT: E 66 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7939 (ttm170) REVERT: E 81 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.8113 (mmm-85) REVERT: E 102 VAL cc_start: 0.8489 (p) cc_final: 0.8232 (m) REVERT: E 105 GLN cc_start: 0.8304 (pm20) cc_final: 0.8011 (pm20) REVERT: I 24 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7678 (mmm-85) REVERT: I 45 LYS cc_start: 0.7770 (tttm) cc_final: 0.7377 (pttp) REVERT: I 79 GLN cc_start: 0.7003 (mm-40) cc_final: 0.6698 (mm110) REVERT: B 138 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: B 416 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8033 (mttp) REVERT: F 6 GLU cc_start: 0.6634 (mp0) cc_final: 0.6405 (mp0) REVERT: F 66 ARG cc_start: 0.8360 (ttp-110) cc_final: 0.7944 (ttm170) REVERT: F 81 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8162 (mmm-85) REVERT: F 96 ASP cc_start: 0.8410 (t70) cc_final: 0.8186 (t70) REVERT: F 102 VAL cc_start: 0.8470 (p) cc_final: 0.8220 (m) REVERT: F 105 GLN cc_start: 0.8291 (pm20) cc_final: 0.8068 (pm20) REVERT: J 24 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7670 (mmm-85) REVERT: J 45 LYS cc_start: 0.7775 (tttm) cc_final: 0.7434 (pttp) REVERT: J 79 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6824 (mm110) REVERT: C 416 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8028 (mttp) REVERT: G 6 GLU cc_start: 0.6623 (mp0) cc_final: 0.6391 (mp0) REVERT: G 66 ARG cc_start: 0.8362 (ttp-110) cc_final: 0.7945 (ttm170) REVERT: G 81 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8159 (mmm-85) REVERT: G 96 ASP cc_start: 0.8353 (t0) cc_final: 0.8110 (t70) REVERT: G 102 VAL cc_start: 0.8470 (p) cc_final: 0.8219 (m) REVERT: G 105 GLN cc_start: 0.8293 (pm20) cc_final: 0.8073 (pm20) REVERT: K 24 ARG cc_start: 0.7915 (ttp80) cc_final: 0.7672 (mmm-85) REVERT: K 45 LYS cc_start: 0.7766 (tttm) cc_final: 0.7425 (pttp) REVERT: K 79 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6779 (mm110) REVERT: D 416 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8031 (mttp) outliers start: 89 outliers final: 61 residues processed: 411 average time/residue: 0.5342 time to fit residues: 251.5478 Evaluate side-chains 430 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 364 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [138, 134, 66, 157, 96, 126, 239, 153, 13, 190, 104] chunk 138 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 239 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 190 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.140683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104667 restraints weight = 25552.550| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.33 r_work: 0.3327 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20020 Z= 0.193 Angle : 0.668 11.655 27172 Z= 0.342 Chirality : 0.047 0.147 2908 Planarity : 0.005 0.079 3456 Dihedral : 5.773 59.149 3080 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.43 % Favored : 96.41 % Rotamer: Outliers : 3.24 % Allowed : 25.63 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.95 (0.17), residues: 2476 helix: None (None), residues: 0 sheet: -0.00 (0.17), residues: 988 loop : -1.08 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 56 TYR 0.013 0.002 TYR C 237 PHE 0.020 0.002 PHE E 78 TRP 0.012 0.001 TRP A 177 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (19964) covalent geometry : angle 0.65608 / 0.34 (27044) SS BOND : bond 0.00358 / 0.25 ( 40) SS BOND : angle 1.10343 / 0.74 ( 80) hydrogen bonds : bond 0.03531 / 2.34 ( 616) hydrogen bonds : angle 5.95871 / 4.19 ( 1740) link_BETA1-4 : bond 0.00270 / 0.16 ( 8) link_BETA1-4 : angle 2.19912 / 1.77 ( 24) link_NAG-ASN : bond 0.00499 / 0.29 ( 8) link_NAG-ASN : angle 3.33826 / 1.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 368 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.8036 (ttp-110) REVERT: H 81 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8118 (mmm-85) REVERT: H 105 GLN cc_start: 0.8305 (pm20) cc_final: 0.7993 (pm20) REVERT: L 24 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7668 (mmm-85) REVERT: L 45 LYS cc_start: 0.7801 (tttm) cc_final: 0.7335 (pttp) REVERT: L 79 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6868 (mm110) REVERT: A 404 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8306 (mmmm) REVERT: A 416 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8058 (mttp) REVERT: E 6 GLU cc_start: 0.6706 (mp0) cc_final: 0.6486 (mp0) REVERT: E 66 ARG cc_start: 0.8393 (ttp-110) cc_final: 0.8038 (ttp-110) REVERT: E 81 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.8114 (mmm-85) REVERT: E 102 VAL cc_start: 0.8521 (p) cc_final: 0.8289 (m) REVERT: E 105 GLN cc_start: 0.8355 (pm20) cc_final: 0.8092 (pm20) REVERT: I 24 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7671 (mmm-85) REVERT: I 45 LYS cc_start: 0.7824 (tttm) cc_final: 0.7571 (pttp) REVERT: I 79 GLN cc_start: 0.7037 (mm-40) cc_final: 0.6822 (mm110) REVERT: B 138 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: B 404 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8304 (mmmm) REVERT: B 416 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8069 (mttp) REVERT: F 66 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.8036 (ttp-110) REVERT: F 81 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8122 (mmm-85) REVERT: F 102 VAL cc_start: 0.8514 (p) cc_final: 0.8264 (m) REVERT: F 105 GLN cc_start: 0.8317 (pm20) cc_final: 0.8000 (pm20) REVERT: J 24 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7664 (mmm-85) REVERT: J 45 LYS cc_start: 0.7836 (tttm) cc_final: 0.7477 (pttp) REVERT: J 79 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6771 (mm110) REVERT: C 171 ILE cc_start: 0.8417 (mp) cc_final: 0.8208 (mp) REVERT: C 404 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8304 (mmmm) REVERT: C 416 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8059 (mttp) REVERT: G 66 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.8038 (ttp-110) REVERT: G 81 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8128 (mmm-85) REVERT: G 96 ASP cc_start: 0.8398 (t0) cc_final: 0.8166 (t70) REVERT: G 102 VAL cc_start: 0.8508 (p) cc_final: 0.8258 (m) REVERT: G 105 GLN cc_start: 0.8314 (pm20) cc_final: 0.7999 (pm20) REVERT: K 24 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7675 (mmm-85) REVERT: K 45 LYS cc_start: 0.7807 (tttm) cc_final: 0.7346 (pttp) REVERT: K 79 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6762 (mm110) REVERT: D 404 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8300 (mmmm) REVERT: D 416 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8061 (mttp) outliers start: 67 outliers final: 54 residues processed: 413 average time/residue: 0.5191 time to fit residues: 246.0371 Evaluate side-chains 411 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 352 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [99, 60, 194, 134, 29, 160, 155, 184, 10, 243, 114] chunk 99 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 194 optimal weight: 0.0770 chunk 134 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 243 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.103032 restraints weight = 25328.965| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.34 r_work: 0.3317 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20020 Z= 0.211 Angle : 0.682 11.890 27172 Z= 0.350 Chirality : 0.047 0.147 2908 Planarity : 0.005 0.089 3456 Dihedral : 5.810 58.948 3080 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.68 % Favored : 96.16 % Rotamer: Outliers : 3.24 % Allowed : 25.48 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.03 (0.17), residues: 2476 helix: None (None), residues: 0 sheet: -0.05 (0.17), residues: 988 loop : -1.14 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG I 56 TYR 0.014 0.002 TYR C 237 PHE 0.019 0.002 PHE E 78 TRP 0.012 0.001 TRP C 177 HIS 0.006 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (19964) covalent geometry : angle 0.67044 / 0.35 (27044) SS BOND : bond 0.00387 / 0.27 ( 40) SS BOND : angle 1.17275 / 0.79 ( 80) hydrogen bonds : bond 0.03586 / 2.38 ( 616) hydrogen bonds : angle 6.00927 / 4.23 ( 1740) link_BETA1-4 : bond 0.00295 / 0.17 ( 8) link_BETA1-4 : angle 2.16725 / 1.73 ( 24) link_NAG-ASN : bond 0.00492 / 0.29 ( 8) link_NAG-ASN : angle 3.36501 / 1.84 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 356 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6694 (mp0) cc_final: 0.6387 (mp0) REVERT: H 66 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.7996 (ttp-110) REVERT: H 81 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8112 (mmm-85) REVERT: L 24 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7670 (mmm-85) REVERT: L 45 LYS cc_start: 0.7794 (tttm) cc_final: 0.7333 (pttp) REVERT: L 79 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6820 (mm110) REVERT: A 416 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8085 (mttp) REVERT: E 6 GLU cc_start: 0.6690 (mp0) cc_final: 0.6408 (mp0) REVERT: E 66 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8002 (ttp-110) REVERT: E 81 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.8114 (mmm-85) REVERT: E 102 VAL cc_start: 0.8525 (p) cc_final: 0.8286 (m) REVERT: E 105 GLN cc_start: 0.8294 (pm20) cc_final: 0.8083 (pm20) REVERT: I 24 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7665 (mmm-85) REVERT: I 45 LYS cc_start: 0.7824 (tttm) cc_final: 0.7395 (pttp) REVERT: I 79 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6775 (mm110) REVERT: B 138 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: B 416 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8085 (mttp) REVERT: F 6 GLU cc_start: 0.6718 (mp0) cc_final: 0.6439 (mp0) REVERT: F 66 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.8005 (ttp-110) REVERT: F 81 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8118 (mmm-85) REVERT: J 24 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7661 (mmm-85) REVERT: J 45 LYS cc_start: 0.7862 (tttm) cc_final: 0.7507 (pttp) REVERT: J 79 GLN cc_start: 0.7014 (mm-40) cc_final: 0.6746 (mm110) REVERT: C 416 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8085 (mttp) REVERT: G 6 GLU cc_start: 0.6703 (mp0) cc_final: 0.6400 (mp0) REVERT: G 66 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.7999 (ttp-110) REVERT: G 81 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8122 (mmm-85) REVERT: G 96 ASP cc_start: 0.8425 (t0) cc_final: 0.8202 (t70) REVERT: K 24 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7672 (mmm-85) REVERT: K 45 LYS cc_start: 0.7813 (tttm) cc_final: 0.7353 (pttp) REVERT: K 79 GLN cc_start: 0.7040 (mm-40) cc_final: 0.6757 (mm110) REVERT: D 171 ILE cc_start: 0.8424 (mp) cc_final: 0.8215 (mp) REVERT: D 416 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8087 (mttp) outliers start: 67 outliers final: 54 residues processed: 401 average time/residue: 0.5216 time to fit residues: 240.3282 Evaluate side-chains 410 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 351 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [126, 185, 100, 195, 19, 119, 12, 1, 157, 102, 173] chunk 126 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.140548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104553 restraints weight = 25745.031| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.33 r_work: 0.3322 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 20020 Z= 0.198 Angle : 0.676 12.214 27172 Z= 0.346 Chirality : 0.047 0.146 2908 Planarity : 0.005 0.086 3456 Dihedral : 5.805 58.942 3080 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.28 % Rotamer: Outliers : 3.34 % Allowed : 25.53 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.99 (0.17), residues: 2476 helix: None (None), residues: 0 sheet: -0.05 (0.17), residues: 988 loop : -1.09 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 56 TYR 0.014 0.002 TYR H 100G PHE 0.019 0.002 PHE F 78 TRP 0.012 0.001 TRP C 177 HIS 0.007 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (19964) covalent geometry : angle 0.66394 / 0.34 (27044) SS BOND : bond 0.00379 / 0.26 ( 40) SS BOND : angle 1.14904 / 0.78 ( 80) hydrogen bonds : bond 0.03528 / 2.34 ( 616) hydrogen bonds : angle 6.00285 / 4.22 ( 1740) link_BETA1-4 : bond 0.00293 / 0.17 ( 8) link_BETA1-4 : angle 2.14338 / 1.70 ( 24) link_NAG-ASN : bond 0.00488 / 0.29 ( 8) link_NAG-ASN : angle 3.33944 / 1.83 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8652.99 seconds wall clock time: 147 minutes 49.38 seconds (8869.38 seconds total)