Starting phenix.real_space_refine on Thu Feb 5 19:58:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyh_46044/02_2026/9cyh_46044.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyh_46044/02_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_46044/02_2026/9cyh_46044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyh_46044/02_2026/9cyh_46044.map" model { file = "/net/cci-nas-00/data/ceres_data/9cyh_46044/02_2026/9cyh_46044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyh_46044/02_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-2.0-5952/lib/python3.9/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: 3.59, per 1000 atoms: 0.18 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=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 830.2 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: 0.93 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: 4.32 Time building geometry restraints manager: 2.30 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: 10458 17.64 - 35.28: 1062 35.28 - 52.93: 264 52.93 - 70.57: 68 70.57 - 88.21: 36 Dihedral angle restraints: 11888 sinusoidal: 4828 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 11885 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: 2.03 - 2.60: 275 2.60 - 3.18: 16187 3.18 - 3.75: 30559 3.75 - 4.33: 46704 4.33 - 4.90: 78061 Nonbonded interactions: 171786 Sorted by model distance: nonbonded pdb=" SG CYS A 182 " pdb=" SG CYS A 229 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS C 182 " pdb=" SG CYS C 229 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS D 182 " pdb=" SG CYS D 229 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS B 182 " pdb=" SG CYS B 229 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS A 277 " pdb=" SG CYS A 291 " model vdw 2.027 3.760 ... (remaining 171781 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: 0.05 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: 12.140 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.710 Find NCS groups from input model: 0.340 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 19980 Z= 0.230 Angle : 0.942 10.117 27092 Z= 0.470 Chirality : 0.053 0.252 2908 Planarity : 0.025 0.381 3456 Dihedral : 16.029 88.208 7440 Min Nonbonded Distance : 2.026 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 covalent geometry : bond 0.00549 (19964) covalent geometry : angle 0.91927 (27044) hydrogen bonds : bond 0.25967 ( 616) hydrogen bonds : angle 10.57105 ( 1740) link_BETA1-4 : bond 0.00114 ( 8) link_BETA1-4 : angle 3.01023 ( 24) link_NAG-ASN : bond 0.00708 ( 8) link_NAG-ASN : angle 6.37134 ( 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 : 0.778 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 528 average time/residue: 0.6100 time to fit residues: 363.9815 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 : 0.742 ------------------------------------------------------------------------------- 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: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN H 40 HIS A 183 HIS A 294 ASN E 16 GLN E 40 HIS B 183 HIS B 294 ASN F 16 GLN F 40 HIS C 183 HIS C 294 ASN G 16 GLN G 40 HIS D 183 HIS D 294 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.140620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.103536 restraints weight = 25364.553| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.47 r_work: 0.3314 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19980 Z= 0.205 Angle : 0.708 8.291 27092 Z= 0.367 Chirality : 0.049 0.152 2908 Planarity : 0.005 0.043 3456 Dihedral : 7.314 58.982 3088 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.07 % Favored : 96.77 % Rotamer: Outliers : 4.74 % Allowed : 19.78 % Favored : 75.48 % 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: -1.48 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.44 (0.17), residues: 924 loop : -1.36 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 38 TYR 0.015 0.002 TYR F 100D PHE 0.017 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 covalent geometry : bond 0.00455 (19964) covalent geometry : angle 0.68560 (27044) hydrogen bonds : bond 0.04698 ( 616) hydrogen bonds : angle 6.98535 ( 1740) link_BETA1-4 : bond 0.00319 ( 8) link_BETA1-4 : angle 2.50642 ( 24) link_NAG-ASN : bond 0.00655 ( 8) link_NAG-ASN : angle 5.51428 ( 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 530 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 432 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.8703 (tttp) cc_final: 0.8402 (mmpt) REVERT: H 81 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.7915 (mmm-85) REVERT: H 102 VAL cc_start: 0.8283 (p) cc_final: 0.8071 (m) REVERT: H 105 GLN cc_start: 0.7209 (pm20) cc_final: 0.6809 (pm20) REVERT: L 24 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7552 (mmm-85) REVERT: A 90 SER cc_start: 0.8408 (t) cc_final: 0.8131 (m) REVERT: A 337 CYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8543 (m) REVERT: E 13 LYS cc_start: 0.8702 (tttp) cc_final: 0.8399 (mmpt) REVERT: E 81 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.7915 (mmm-85) REVERT: E 102 VAL cc_start: 0.8319 (p) cc_final: 0.8108 (m) REVERT: E 105 GLN cc_start: 0.7216 (pm20) cc_final: 0.6811 (pm20) REVERT: I 24 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7555 (mmm-85) REVERT: B 90 SER cc_start: 0.8401 (t) cc_final: 0.8123 (m) REVERT: B 337 CYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8545 (m) REVERT: F 13 LYS cc_start: 0.8701 (tttp) cc_final: 0.8398 (mmpt) REVERT: F 81 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.7914 (mmm-85) REVERT: F 102 VAL cc_start: 0.8320 (p) cc_final: 0.8108 (m) REVERT: F 105 GLN cc_start: 0.7225 (pm20) cc_final: 0.6824 (pm20) REVERT: J 24 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7553 (mmm-85) REVERT: C 90 SER cc_start: 0.8404 (t) cc_final: 0.8126 (m) REVERT: C 337 CYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8539 (m) REVERT: G 13 LYS cc_start: 0.8703 (tttp) cc_final: 0.8400 (mmpt) REVERT: G 81 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.7911 (mmm-85) REVERT: G 102 VAL cc_start: 0.8283 (p) cc_final: 0.8070 (m) REVERT: G 105 GLN cc_start: 0.7225 (pm20) cc_final: 0.6823 (pm20) REVERT: K 24 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7551 (mmm-85) REVERT: D 90 SER cc_start: 0.8401 (t) cc_final: 0.8123 (m) REVERT: D 337 CYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8544 (m) REVERT: D 377 MET cc_start: 0.8164 (tpp) cc_final: 0.7886 (tpp) outliers start: 98 outliers final: 54 residues processed: 464 average time/residue: 0.5884 time to fit residues: 310.6815 Evaluate side-chains 482 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 424 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 ASP 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 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 110 THR Chi-restraints excluded: chain I residue 22 THR 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 198 ASN 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 110 THR Chi-restraints excluded: chain J residue 22 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 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 110 THR Chi-restraints excluded: chain K residue 22 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 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: chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 121 optimal weight: 0.0170 chunk 226 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS B 431 HIS C 431 HIS D 431 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.140418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.102895 restraints weight = 25664.799| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.48 r_work: 0.3314 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19980 Z= 0.178 Angle : 0.641 7.215 27092 Z= 0.334 Chirality : 0.047 0.160 2908 Planarity : 0.005 0.041 3456 Dihedral : 6.708 59.536 3080 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.43 % Favored : 96.41 % Rotamer: Outliers : 4.84 % Allowed : 20.84 % Favored : 74.32 % 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: -1.29 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.34 (0.17), residues: 928 loop : -1.21 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 56 TYR 0.012 0.001 TYR H 50 PHE 0.019 0.002 PHE F 78 TRP 0.012 0.001 TRP A 177 HIS 0.007 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00400 (19964) covalent geometry : angle 0.62561 (27044) hydrogen bonds : bond 0.04089 ( 616) hydrogen bonds : angle 6.34594 ( 1740) link_BETA1-4 : bond 0.00236 ( 8) link_BETA1-4 : angle 2.32686 ( 24) link_NAG-ASN : bond 0.00521 ( 8) link_NAG-ASN : angle 4.16486 ( 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 522 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 422 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6203 (mp0) cc_final: 0.5996 (mp0) REVERT: H 13 LYS cc_start: 0.8691 (tttp) cc_final: 0.8397 (mmpt) REVERT: H 66 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.7959 (ttm170) REVERT: H 81 ARG cc_start: 0.8636 (mmm-85) cc_final: 0.8309 (mmm-85) REVERT: H 105 GLN cc_start: 0.7479 (pm20) cc_final: 0.6997 (pm20) REVERT: L 24 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7699 (mmm-85) REVERT: L 79 GLN cc_start: 0.7113 (mm-40) cc_final: 0.6744 (mm110) REVERT: A 90 SER cc_start: 0.8523 (t) cc_final: 0.8233 (m) REVERT: A 138 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: A 337 CYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8573 (m) REVERT: A 416 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8175 (mttp) REVERT: E 6 GLU cc_start: 0.6220 (mp0) cc_final: 0.6012 (mp0) REVERT: E 13 LYS cc_start: 0.8692 (tttp) cc_final: 0.8395 (mmpt) REVERT: E 66 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7966 (ttm170) REVERT: E 81 ARG cc_start: 0.8636 (mmm-85) cc_final: 0.8309 (mmm-85) REVERT: E 105 GLN cc_start: 0.7491 (pm20) cc_final: 0.7005 (pm20) REVERT: I 24 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7722 (mmm-85) REVERT: I 79 GLN cc_start: 0.7104 (mm-40) cc_final: 0.6782 (mm110) REVERT: B 90 SER cc_start: 0.8522 (t) cc_final: 0.8233 (m) REVERT: B 138 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: B 337 CYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8571 (m) REVERT: B 416 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8173 (mttp) REVERT: F 6 GLU cc_start: 0.6252 (mp0) cc_final: 0.6038 (mp0) REVERT: F 13 LYS cc_start: 0.8693 (tttp) cc_final: 0.8397 (mmpt) REVERT: F 66 ARG cc_start: 0.8338 (ttp-110) cc_final: 0.7970 (ttm170) REVERT: F 81 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8313 (mmm-85) REVERT: F 105 GLN cc_start: 0.7491 (pm20) cc_final: 0.7004 (pm20) REVERT: J 24 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7695 (mmm-85) REVERT: J 79 GLN cc_start: 0.7079 (mm-40) cc_final: 0.6754 (mm110) REVERT: C 90 SER cc_start: 0.8523 (t) cc_final: 0.8234 (m) REVERT: C 138 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: C 337 CYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8570 (m) REVERT: C 416 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8172 (mttp) REVERT: G 6 GLU cc_start: 0.6226 (mp0) cc_final: 0.6017 (mp0) REVERT: G 13 LYS cc_start: 0.8692 (tttp) cc_final: 0.8396 (mmpt) REVERT: G 66 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.7969 (ttm170) REVERT: G 81 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8308 (mmm-85) REVERT: G 105 GLN cc_start: 0.7484 (pm20) cc_final: 0.7001 (pm20) REVERT: K 24 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7726 (mmm-85) REVERT: K 79 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6822 (mm110) REVERT: D 90 SER cc_start: 0.8527 (t) cc_final: 0.8240 (m) REVERT: D 138 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: D 337 CYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8573 (m) REVERT: D 377 MET cc_start: 0.8219 (tpp) cc_final: 0.7986 (tpp) REVERT: D 416 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8165 (mttp) outliers start: 100 outliers final: 53 residues processed: 466 average time/residue: 0.4967 time to fit residues: 263.6818 Evaluate side-chains 483 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 418 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 178 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 195 optimal weight: 0.0040 chunk 207 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.139202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101688 restraints weight = 25766.282| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.48 r_work: 0.3297 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19980 Z= 0.206 Angle : 0.651 7.509 27092 Z= 0.337 Chirality : 0.047 0.150 2908 Planarity : 0.005 0.043 3456 Dihedral : 6.428 59.327 3080 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.12 % Rotamer: Outliers : 4.74 % Allowed : 21.47 % Favored : 73.79 % 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: -1.22 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.28 (0.17), residues: 920 loop : -1.16 (0.14), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 56 TYR 0.012 0.001 TYR F 100D PHE 0.021 0.002 PHE F 78 TRP 0.011 0.001 TRP B 177 HIS 0.007 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00467 (19964) covalent geometry : angle 0.63855 (27044) hydrogen bonds : bond 0.03830 ( 616) hydrogen bonds : angle 6.26744 ( 1740) link_BETA1-4 : bond 0.00245 ( 8) link_BETA1-4 : angle 2.30649 ( 24) link_NAG-ASN : bond 0.00497 ( 8) link_NAG-ASN : angle 3.70984 ( 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 516 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 418 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.8696 (tttp) cc_final: 0.8386 (mmpt) REVERT: H 66 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.7897 (ttm170) REVERT: H 81 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8238 (mmm-85) REVERT: H 96 ASP cc_start: 0.8265 (t0) cc_final: 0.7956 (t70) REVERT: H 105 GLN cc_start: 0.7440 (pm20) cc_final: 0.6987 (pm20) REVERT: L 24 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7738 (mmm-85) REVERT: L 79 GLN cc_start: 0.7025 (mm-40) cc_final: 0.6698 (mm110) REVERT: A 90 SER cc_start: 0.8580 (t) cc_final: 0.8317 (m) REVERT: A 138 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: A 337 CYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8638 (m) REVERT: A 416 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8141 (mttp) REVERT: E 13 LYS cc_start: 0.8696 (tttp) cc_final: 0.8388 (mmpt) REVERT: E 66 ARG cc_start: 0.8354 (ttp-110) cc_final: 0.7906 (ttm170) REVERT: E 81 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8241 (mmm-85) REVERT: E 96 ASP cc_start: 0.8260 (t0) cc_final: 0.7969 (t70) REVERT: E 105 GLN cc_start: 0.7437 (pm20) cc_final: 0.6977 (pm20) REVERT: I 24 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7755 (mmm-85) REVERT: I 79 GLN cc_start: 0.7050 (mm-40) cc_final: 0.6698 (mm110) REVERT: B 90 SER cc_start: 0.8579 (t) cc_final: 0.8317 (m) REVERT: B 138 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: B 337 CYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8633 (m) REVERT: B 416 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8136 (mttp) REVERT: F 13 LYS cc_start: 0.8698 (tttp) cc_final: 0.8388 (mmpt) REVERT: F 66 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.7911 (ttm170) REVERT: F 81 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.8243 (mmm-85) REVERT: F 96 ASP cc_start: 0.8266 (t0) cc_final: 0.7956 (t70) REVERT: F 105 GLN cc_start: 0.7433 (pm20) cc_final: 0.6977 (pm20) REVERT: J 24 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7743 (mmm-85) REVERT: J 79 GLN cc_start: 0.7031 (mm-40) cc_final: 0.6679 (mm110) REVERT: C 90 SER cc_start: 0.8568 (t) cc_final: 0.8306 (m) REVERT: C 138 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: C 337 CYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8632 (m) REVERT: C 416 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8135 (mttp) REVERT: G 13 LYS cc_start: 0.8696 (tttp) cc_final: 0.8386 (mmpt) REVERT: G 66 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.7906 (ttm170) REVERT: G 81 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.8236 (mmm-85) REVERT: G 96 ASP cc_start: 0.8269 (t0) cc_final: 0.7954 (t70) REVERT: G 105 GLN cc_start: 0.7440 (pm20) cc_final: 0.6979 (pm20) REVERT: K 24 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7746 (mmm-85) REVERT: K 79 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6639 (mm110) REVERT: D 90 SER cc_start: 0.8579 (t) cc_final: 0.8315 (m) REVERT: D 138 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: D 337 CYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8636 (m) REVERT: D 416 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8132 (mttp) outliers start: 98 outliers final: 62 residues processed: 460 average time/residue: 0.4965 time to fit residues: 261.5026 Evaluate side-chains 478 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 404 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 22 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 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 244 SER 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 22 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 135 TYR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 244 SER 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 22 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 135 TYR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 244 SER 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 22 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 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 244 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 201 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.140454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.103551 restraints weight = 25424.244| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.45 r_work: 0.3316 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19980 Z= 0.164 Angle : 0.623 7.864 27092 Z= 0.322 Chirality : 0.046 0.150 2908 Planarity : 0.005 0.053 3456 Dihedral : 6.015 59.403 3080 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.28 % Rotamer: Outliers : 4.59 % Allowed : 22.63 % Favored : 72.78 % 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: -1.09 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.25 (0.17), residues: 940 loop : -1.03 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 56 TYR 0.012 0.001 TYR F 100D PHE 0.020 0.002 PHE F 78 TRP 0.011 0.001 TRP A 177 HIS 0.007 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00371 (19964) covalent geometry : angle 0.61147 (27044) hydrogen bonds : bond 0.03552 ( 616) hydrogen bonds : angle 6.03001 ( 1740) link_BETA1-4 : bond 0.00280 ( 8) link_BETA1-4 : angle 2.31797 ( 24) link_NAG-ASN : bond 0.00521 ( 8) link_NAG-ASN : angle 3.46827 ( 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 512 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 417 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.8696 (tttp) cc_final: 0.8392 (mmpt) REVERT: H 66 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.7987 (ttm170) REVERT: H 81 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8167 (mmm-85) REVERT: H 102 VAL cc_start: 0.8343 (p) cc_final: 0.8088 (m) REVERT: H 105 GLN cc_start: 0.7665 (pm20) cc_final: 0.7202 (pm20) REVERT: L 24 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7695 (mmm-85) REVERT: L 79 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6717 (mm110) REVERT: A 90 SER cc_start: 0.8579 (t) cc_final: 0.8328 (m) REVERT: A 138 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: A 416 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8117 (mttp) REVERT: A 420 CYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7277 (p) REVERT: E 13 LYS cc_start: 0.8697 (tttp) cc_final: 0.8393 (mmpt) REVERT: E 66 ARG cc_start: 0.8369 (ttp-110) cc_final: 0.7986 (ttm170) REVERT: E 81 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8172 (mmm-85) REVERT: E 102 VAL cc_start: 0.8330 (p) cc_final: 0.8076 (m) REVERT: E 105 GLN cc_start: 0.7638 (pm20) cc_final: 0.7165 (pm20) REVERT: I 24 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7726 (mmm-85) REVERT: I 79 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6732 (mm110) REVERT: B 90 SER cc_start: 0.8576 (t) cc_final: 0.8322 (m) REVERT: B 138 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: B 416 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8121 (mttp) REVERT: B 420 CYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7263 (p) REVERT: F 13 LYS cc_start: 0.8699 (tttp) cc_final: 0.8395 (mmpt) REVERT: F 66 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.7996 (ttm170) REVERT: F 81 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8176 (mmm-85) REVERT: F 102 VAL cc_start: 0.8350 (p) cc_final: 0.8096 (m) REVERT: F 105 GLN cc_start: 0.7638 (pm20) cc_final: 0.7164 (pm20) REVERT: J 24 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7703 (mmm-85) REVERT: J 79 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6735 (mm110) REVERT: C 90 SER cc_start: 0.8580 (t) cc_final: 0.8327 (m) REVERT: C 138 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: C 416 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8124 (mttp) REVERT: C 420 CYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7249 (p) REVERT: G 13 LYS cc_start: 0.8695 (tttp) cc_final: 0.8391 (mmpt) REVERT: G 66 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.7994 (ttm170) REVERT: G 81 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8169 (mmm-85) REVERT: G 102 VAL cc_start: 0.8365 (p) cc_final: 0.8112 (m) REVERT: G 105 GLN cc_start: 0.7654 (pm20) cc_final: 0.7181 (pm20) REVERT: K 24 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7732 (mmm-85) REVERT: K 79 GLN cc_start: 0.7009 (mm-40) cc_final: 0.6697 (mm110) REVERT: D 90 SER cc_start: 0.8576 (t) cc_final: 0.8322 (m) REVERT: D 138 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: D 416 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8121 (mttp) REVERT: D 420 CYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7267 (p) outliers start: 95 outliers final: 60 residues processed: 457 average time/residue: 0.5638 time to fit residues: 293.0513 Evaluate side-chains 479 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 407 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 21 ILE 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 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 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 420 CYS 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 110 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 81 ASP 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 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 420 CYS 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 110 THR Chi-restraints excluded: chain J residue 21 ILE 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 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 420 CYS 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 110 THR Chi-restraints excluded: chain K residue 21 ILE 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 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 420 CYS 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: chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 205 optimal weight: 0.0270 chunk 60 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.140967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.104769 restraints weight = 25614.578| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.39 r_work: 0.3343 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19980 Z= 0.170 Angle : 0.630 9.807 27092 Z= 0.324 Chirality : 0.045 0.144 2908 Planarity : 0.005 0.056 3456 Dihedral : 5.813 59.062 3080 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.12 % Rotamer: Outliers : 4.06 % Allowed : 22.92 % Favored : 73.02 % 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: -1.01 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.13 (0.17), residues: 972 loop : -1.04 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 56 TYR 0.011 0.001 TYR F 100D PHE 0.019 0.002 PHE G 78 TRP 0.010 0.001 TRP D 177 HIS 0.007 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00386 (19964) covalent geometry : angle 0.61895 (27044) hydrogen bonds : bond 0.03473 ( 616) hydrogen bonds : angle 5.93296 ( 1740) link_BETA1-4 : bond 0.00287 ( 8) link_BETA1-4 : angle 2.30546 ( 24) link_NAG-ASN : bond 0.00517 ( 8) link_NAG-ASN : angle 3.39374 ( 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 491 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 407 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6756 (mp0) cc_final: 0.6487 (mp0) REVERT: H 13 LYS cc_start: 0.8705 (tttp) cc_final: 0.8388 (mmpt) REVERT: H 66 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.7955 (ttm170) REVERT: H 81 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8139 (mmm-85) REVERT: H 102 VAL cc_start: 0.8431 (p) cc_final: 0.8174 (m) REVERT: H 105 GLN cc_start: 0.7938 (pm20) cc_final: 0.7637 (pm20) REVERT: L 24 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7776 (mmm-85) REVERT: L 79 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6770 (mm110) REVERT: A 90 SER cc_start: 0.8651 (t) cc_final: 0.8434 (m) REVERT: A 138 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: A 289 CYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8576 (m) REVERT: A 416 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8135 (mttp) REVERT: A 420 CYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7398 (p) REVERT: E 6 GLU cc_start: 0.6781 (mp0) cc_final: 0.6507 (mp0) REVERT: E 13 LYS cc_start: 0.8705 (tttp) cc_final: 0.8387 (mmpt) REVERT: E 66 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.7974 (ttm170) REVERT: E 81 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.8135 (mmm-85) REVERT: E 96 ASP cc_start: 0.8408 (t70) cc_final: 0.8168 (t70) REVERT: E 102 VAL cc_start: 0.8432 (p) cc_final: 0.8174 (m) REVERT: E 105 GLN cc_start: 0.7934 (pm20) cc_final: 0.7634 (pm20) REVERT: I 24 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7789 (mmm-85) REVERT: I 79 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6754 (mm110) REVERT: B 90 SER cc_start: 0.8650 (t) cc_final: 0.8432 (m) REVERT: B 138 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: B 289 CYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8595 (m) REVERT: B 416 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8131 (mttp) REVERT: B 420 CYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7396 (p) REVERT: F 6 GLU cc_start: 0.6780 (mp0) cc_final: 0.6509 (mp0) REVERT: F 13 LYS cc_start: 0.8706 (tttp) cc_final: 0.8387 (mmpt) REVERT: F 66 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.7977 (ttm170) REVERT: F 81 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8141 (mmm-85) REVERT: F 96 ASP cc_start: 0.8388 (t70) cc_final: 0.8140 (t70) REVERT: F 102 VAL cc_start: 0.8441 (p) cc_final: 0.8184 (m) REVERT: F 105 GLN cc_start: 0.7929 (pm20) cc_final: 0.7625 (pm20) REVERT: J 24 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7776 (mmm-85) REVERT: J 79 GLN cc_start: 0.7079 (mm-40) cc_final: 0.6704 (mm110) REVERT: C 90 SER cc_start: 0.8648 (t) cc_final: 0.8431 (m) REVERT: C 138 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: C 289 CYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8598 (m) REVERT: C 416 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8126 (mttp) REVERT: C 420 CYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7396 (p) REVERT: G 6 GLU cc_start: 0.6771 (mp0) cc_final: 0.6494 (mp0) REVERT: G 13 LYS cc_start: 0.8706 (tttp) cc_final: 0.8387 (mmpt) REVERT: G 66 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.7969 (ttm170) REVERT: G 81 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8136 (mmm-85) REVERT: G 96 ASP cc_start: 0.8384 (t70) cc_final: 0.8136 (t70) REVERT: G 102 VAL cc_start: 0.8438 (p) cc_final: 0.8179 (m) REVERT: G 105 GLN cc_start: 0.7937 (pm20) cc_final: 0.7638 (pm20) REVERT: K 24 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7774 (mmm-85) REVERT: K 79 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6708 (mm110) REVERT: D 90 SER cc_start: 0.8649 (t) cc_final: 0.8435 (m) REVERT: D 138 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: D 289 CYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8603 (m) REVERT: D 416 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8130 (mttp) REVERT: D 420 CYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7406 (p) outliers start: 84 outliers final: 49 residues processed: 454 average time/residue: 0.5672 time to fit residues: 294.6361 Evaluate side-chains 439 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 374 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 LEU 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 289 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 420 CYS 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 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 289 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 420 CYS 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 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 135 TYR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 289 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 420 CYS 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 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 289 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 420 CYS 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: chunk 139 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 234 optimal weight: 0.9990 chunk 229 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.140796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.104392 restraints weight = 25734.354| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.43 r_work: 0.3341 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19980 Z= 0.169 Angle : 0.633 10.790 27092 Z= 0.325 Chirality : 0.046 0.143 2908 Planarity : 0.005 0.063 3456 Dihedral : 5.729 59.181 3080 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.76 % Favored : 96.08 % Rotamer: Outliers : 4.50 % Allowed : 23.31 % Favored : 72.20 % 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: -1.00 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.15 (0.17), residues: 976 loop : -1.02 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 56 TYR 0.011 0.001 TYR F 50 PHE 0.019 0.002 PHE G 78 TRP 0.011 0.001 TRP D 177 HIS 0.007 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00385 (19964) covalent geometry : angle 0.62187 (27044) hydrogen bonds : bond 0.03432 ( 616) hydrogen bonds : angle 5.87882 ( 1740) link_BETA1-4 : bond 0.00303 ( 8) link_BETA1-4 : angle 2.27232 ( 24) link_NAG-ASN : bond 0.00526 ( 8) link_NAG-ASN : angle 3.34375 ( 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 486 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 393 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6756 (mp0) cc_final: 0.6501 (mp0) REVERT: H 66 ARG cc_start: 0.8386 (ttp-110) cc_final: 0.8112 (ttp-110) REVERT: H 81 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8130 (mmm-85) REVERT: H 96 ASP cc_start: 0.8356 (t70) cc_final: 0.8102 (t70) REVERT: H 102 VAL cc_start: 0.8375 (p) cc_final: 0.8118 (m) REVERT: H 105 GLN cc_start: 0.7897 (pm20) cc_final: 0.7559 (pm20) REVERT: L 24 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7786 (mmm-85) REVERT: L 45 LYS cc_start: 0.7736 (tttm) cc_final: 0.7316 (pttp) REVERT: L 79 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6703 (mm110) REVERT: A 90 SER cc_start: 0.8650 (t) cc_final: 0.8431 (m) REVERT: A 138 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: A 289 CYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8579 (m) REVERT: A 416 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8115 (mttp) REVERT: A 420 CYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7367 (p) REVERT: E 6 GLU cc_start: 0.6775 (mp0) cc_final: 0.6512 (mp0) REVERT: E 66 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.8128 (ttp-110) REVERT: E 81 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8129 (mmm-85) REVERT: E 96 ASP cc_start: 0.8377 (t70) cc_final: 0.8088 (t70) REVERT: E 102 VAL cc_start: 0.8370 (p) cc_final: 0.8111 (m) REVERT: E 105 GLN cc_start: 0.7887 (pm20) cc_final: 0.7548 (pm20) REVERT: I 24 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7786 (mmm-85) REVERT: I 45 LYS cc_start: 0.7752 (tttm) cc_final: 0.7340 (pttp) REVERT: I 79 GLN cc_start: 0.7036 (mm-40) cc_final: 0.6637 (mm110) REVERT: B 90 SER cc_start: 0.8650 (t) cc_final: 0.8432 (m) REVERT: B 138 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: B 289 CYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8571 (m) REVERT: B 416 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8105 (mttp) REVERT: B 420 CYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7382 (p) REVERT: F 6 GLU cc_start: 0.6768 (mp0) cc_final: 0.6507 (mp0) REVERT: F 66 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.8124 (ttp-110) REVERT: F 81 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8132 (mmm-85) REVERT: F 96 ASP cc_start: 0.8368 (t70) cc_final: 0.8074 (t70) REVERT: F 102 VAL cc_start: 0.8378 (p) cc_final: 0.8121 (m) REVERT: F 105 GLN cc_start: 0.7881 (pm20) cc_final: 0.7540 (pm20) REVERT: J 24 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7776 (mmm-85) REVERT: J 42 LYS cc_start: 0.8010 (pttp) cc_final: 0.7784 (pmtt) REVERT: J 45 LYS cc_start: 0.7749 (tttm) cc_final: 0.7328 (pttp) REVERT: J 79 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6735 (mm110) REVERT: C 90 SER cc_start: 0.8642 (t) cc_final: 0.8425 (m) REVERT: C 138 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: C 289 CYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8577 (m) REVERT: C 416 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8106 (mttp) REVERT: C 420 CYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7380 (p) REVERT: G 6 GLU cc_start: 0.6759 (mp0) cc_final: 0.6497 (mp0) REVERT: G 66 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8121 (ttp-110) REVERT: G 81 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8125 (mmm-85) REVERT: G 96 ASP cc_start: 0.8380 (t70) cc_final: 0.8101 (t70) REVERT: G 102 VAL cc_start: 0.8438 (p) cc_final: 0.8180 (m) REVERT: G 105 GLN cc_start: 0.7890 (pm20) cc_final: 0.7549 (pm20) REVERT: K 24 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7780 (mmm-85) REVERT: K 39 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7648 (mmtt) REVERT: K 45 LYS cc_start: 0.7781 (tttm) cc_final: 0.7368 (pttp) REVERT: K 79 GLN cc_start: 0.7014 (mm-40) cc_final: 0.6719 (mm110) REVERT: D 90 SER cc_start: 0.8643 (t) cc_final: 0.8427 (m) REVERT: D 138 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: D 289 CYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8585 (m) REVERT: D 416 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8113 (mttp) REVERT: D 420 CYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7391 (p) outliers start: 93 outliers final: 55 residues processed: 443 average time/residue: 0.5872 time to fit residues: 295.7927 Evaluate side-chains 457 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 386 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 5 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 135 TYR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 289 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 420 CYS 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 5 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 135 TYR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 289 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 420 CYS 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 5 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 135 TYR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 289 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 420 CYS 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 5 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 135 TYR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 289 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 420 CYS Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099275 restraints weight = 26115.559| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.35 r_work: 0.3265 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 19980 Z= 0.369 Angle : 0.754 10.471 27092 Z= 0.391 Chirality : 0.050 0.155 2908 Planarity : 0.006 0.074 3456 Dihedral : 6.187 59.244 3080 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 4.84 % Allowed : 23.74 % Favored : 71.42 % 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: -1.11 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.22 (0.17), residues: 976 loop : -1.10 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 56 TYR 0.017 0.002 TYR D 383 PHE 0.022 0.003 PHE G 78 TRP 0.013 0.002 TRP A 177 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00848 (19964) covalent geometry : angle 0.74365 (27044) hydrogen bonds : bond 0.04084 ( 616) hydrogen bonds : angle 6.21778 ( 1740) link_BETA1-4 : bond 0.00242 ( 8) link_BETA1-4 : angle 2.21100 ( 24) link_NAG-ASN : bond 0.00418 ( 8) link_NAG-ASN : angle 3.62936 ( 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 499 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 399 time to evaluate : 0.770 Fit side-chains REVERT: H 6 GLU cc_start: 0.6786 (mp0) cc_final: 0.6583 (mp0) REVERT: H 66 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.8083 (ttp-110) REVERT: H 81 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8147 (mmm-85) REVERT: H 96 ASP cc_start: 0.8449 (t70) cc_final: 0.8238 (t70) REVERT: H 105 GLN cc_start: 0.7985 (pm20) cc_final: 0.7610 (pm20) REVERT: L 24 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7805 (mmm-85) REVERT: L 45 LYS cc_start: 0.7842 (tttm) cc_final: 0.7406 (pttp) REVERT: L 79 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6694 (mm110) REVERT: A 138 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: A 289 CYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8641 (m) REVERT: A 416 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8274 (mttp) REVERT: A 420 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7550 (p) REVERT: E 6 GLU cc_start: 0.6810 (mp0) cc_final: 0.6606 (mp0) REVERT: E 66 ARG cc_start: 0.8462 (ttp-110) cc_final: 0.8077 (ttp-110) REVERT: E 81 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.8149 (mmm-85) REVERT: E 96 ASP cc_start: 0.8457 (t70) cc_final: 0.8256 (t70) REVERT: E 105 GLN cc_start: 0.7986 (pm20) cc_final: 0.7613 (pm20) REVERT: I 24 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7829 (mmm-85) REVERT: I 45 LYS cc_start: 0.7855 (tttm) cc_final: 0.7418 (pttp) REVERT: I 79 GLN cc_start: 0.6955 (mm-40) cc_final: 0.6708 (mm110) REVERT: B 138 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: B 289 CYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8643 (m) REVERT: B 416 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8283 (mttp) REVERT: B 420 CYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7564 (p) REVERT: F 6 GLU cc_start: 0.6799 (mp0) cc_final: 0.6590 (mp0) REVERT: F 66 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.8079 (ttp-110) REVERT: F 81 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8153 (mmm-85) REVERT: F 96 ASP cc_start: 0.8445 (t70) cc_final: 0.8232 (t70) REVERT: F 105 GLN cc_start: 0.7980 (pm20) cc_final: 0.7606 (pm20) REVERT: J 24 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7812 (mmm-85) REVERT: J 45 LYS cc_start: 0.7851 (tttm) cc_final: 0.7415 (pttp) REVERT: J 79 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6687 (mm110) REVERT: C 138 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: C 171 ILE cc_start: 0.8461 (mp) cc_final: 0.8250 (mp) REVERT: C 289 CYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8643 (m) REVERT: C 416 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8274 (mttp) REVERT: C 420 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7559 (p) REVERT: G 6 GLU cc_start: 0.6796 (mp0) cc_final: 0.6584 (mp0) REVERT: G 66 ARG cc_start: 0.8461 (ttp-110) cc_final: 0.8073 (ttp-110) REVERT: G 81 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8146 (mmm-85) REVERT: G 96 ASP cc_start: 0.8463 (t70) cc_final: 0.8259 (t70) REVERT: G 105 GLN cc_start: 0.7985 (pm20) cc_final: 0.7612 (pm20) REVERT: K 24 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7812 (mmm-85) REVERT: K 45 LYS cc_start: 0.7875 (tttm) cc_final: 0.7443 (pttp) REVERT: K 79 GLN cc_start: 0.7012 (mm-40) cc_final: 0.6638 (mm110) REVERT: D 138 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: D 171 ILE cc_start: 0.8460 (mp) cc_final: 0.8251 (mp) REVERT: D 289 CYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8645 (m) REVERT: D 416 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8274 (mttp) REVERT: D 420 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7553 (p) outliers start: 100 outliers final: 62 residues processed: 453 average time/residue: 0.5680 time to fit residues: 294.0680 Evaluate side-chains 457 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 379 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 5 THR Chi-restraints excluded: chain L residue 22 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 135 TYR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 289 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 420 CYS 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 5 THR Chi-restraints excluded: chain I residue 22 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 244 SER Chi-restraints excluded: chain B residue 289 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 420 CYS 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 5 THR Chi-restraints excluded: chain J residue 22 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 244 SER Chi-restraints excluded: chain C residue 289 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 420 CYS 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 5 THR Chi-restraints excluded: chain K residue 22 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 135 TYR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 289 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 420 CYS 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: chunk 138 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.140357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.103814 restraints weight = 25502.670| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.40 r_work: 0.3334 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19980 Z= 0.161 Angle : 0.654 11.763 27092 Z= 0.335 Chirality : 0.046 0.141 2908 Planarity : 0.005 0.080 3456 Dihedral : 5.873 59.379 3080 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.35 % Favored : 96.49 % Rotamer: Outliers : 3.48 % Allowed : 25.15 % Favored : 71.37 % 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: -1.05 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.24 (0.17), residues: 980 loop : -1.00 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 56 TYR 0.012 0.002 TYR A 237 PHE 0.019 0.002 PHE G 78 TRP 0.014 0.001 TRP A 177 HIS 0.007 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00368 (19964) covalent geometry : angle 0.64301 (27044) hydrogen bonds : bond 0.03446 ( 616) hydrogen bonds : angle 5.96916 ( 1740) link_BETA1-4 : bond 0.00279 ( 8) link_BETA1-4 : angle 2.20507 ( 24) link_NAG-ASN : bond 0.00485 ( 8) link_NAG-ASN : angle 3.41239 ( 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 450 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 378 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 ARG cc_start: 0.8413 (ttp-110) cc_final: 0.7962 (ttp-110) REVERT: H 81 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8120 (mmm-85) REVERT: H 105 GLN cc_start: 0.8017 (pm20) cc_final: 0.7647 (pm20) REVERT: L 24 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7732 (mmm-85) REVERT: L 45 LYS cc_start: 0.7736 (tttm) cc_final: 0.7292 (pttp) REVERT: L 79 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6645 (mm110) REVERT: A 138 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: A 289 CYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8618 (m) REVERT: A 416 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8110 (mttp) REVERT: A 420 CYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7413 (p) REVERT: E 66 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.7977 (ttp-110) REVERT: E 81 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8117 (mmm-85) REVERT: E 96 ASP cc_start: 0.8402 (t70) cc_final: 0.8073 (t70) REVERT: E 105 GLN cc_start: 0.8008 (pm20) cc_final: 0.7636 (pm20) REVERT: I 39 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7390 (mmmt) REVERT: I 45 LYS cc_start: 0.7757 (tttm) cc_final: 0.7313 (pttp) REVERT: I 79 GLN cc_start: 0.6980 (mm-40) cc_final: 0.6519 (mm110) REVERT: B 138 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: B 289 CYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8601 (m) REVERT: B 416 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8081 (mttp) REVERT: B 420 CYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7414 (p) REVERT: F 66 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.7978 (ttp-110) REVERT: F 81 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8118 (mmm-85) REVERT: F 96 ASP cc_start: 0.8392 (t70) cc_final: 0.8061 (t70) REVERT: F 105 GLN cc_start: 0.7994 (pm20) cc_final: 0.7619 (pm20) REVERT: J 24 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7737 (mmm-85) REVERT: J 45 LYS cc_start: 0.7772 (tttm) cc_final: 0.7312 (pttp) REVERT: J 79 GLN cc_start: 0.7014 (mm-40) cc_final: 0.6621 (mm110) REVERT: C 138 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: C 289 CYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8606 (m) REVERT: C 416 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8109 (mttp) REVERT: C 420 CYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7413 (p) REVERT: G 66 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.7973 (ttp-110) REVERT: G 81 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8116 (mmm-85) REVERT: G 96 ASP cc_start: 0.8428 (t70) cc_final: 0.8170 (t70) REVERT: G 105 GLN cc_start: 0.8007 (pm20) cc_final: 0.7635 (pm20) REVERT: K 24 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7746 (mmm-85) REVERT: K 39 LYS cc_start: 0.7895 (mmtm) cc_final: 0.7571 (mmmt) REVERT: K 45 LYS cc_start: 0.7773 (tttm) cc_final: 0.7486 (pttp) REVERT: K 79 GLN cc_start: 0.7008 (mm-40) cc_final: 0.6727 (mm110) REVERT: D 138 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: D 289 CYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8604 (m) REVERT: D 416 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8113 (mttp) REVERT: D 420 CYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7416 (p) outliers start: 72 outliers final: 34 residues processed: 424 average time/residue: 0.5283 time to fit residues: 254.7712 Evaluate side-chains 420 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 369 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 5 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 138 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 289 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain K residue 5 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 138 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 289 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 99 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 194 optimal weight: 0.0570 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3868 r_free = 0.3868 target = 0.136817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100375 restraints weight = 25939.593| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.35 r_work: 0.3279 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 19980 Z= 0.330 Angle : 0.748 11.848 27092 Z= 0.386 Chirality : 0.049 0.145 2908 Planarity : 0.006 0.089 3456 Dihedral : 6.112 58.701 3080 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.52 % Rotamer: Outliers : 3.05 % Allowed : 25.44 % Favored : 71.52 % 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: -1.14 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.26 (0.17), residues: 976 loop : -1.10 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG K 56 TYR 0.014 0.002 TYR C 383 PHE 0.022 0.003 PHE G 78 TRP 0.013 0.002 TRP A 177 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00758 (19964) covalent geometry : angle 0.73806 (27044) hydrogen bonds : bond 0.03956 ( 616) hydrogen bonds : angle 6.18730 ( 1740) link_BETA1-4 : bond 0.00236 ( 8) link_BETA1-4 : angle 2.17734 ( 24) link_NAG-ASN : bond 0.00405 ( 8) link_NAG-ASN : angle 3.53129 ( 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 426 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 363 time to evaluate : 0.634 Fit side-chains REVERT: H 6 GLU cc_start: 0.6782 (mp0) cc_final: 0.6527 (mp0) REVERT: H 66 ARG cc_start: 0.8431 (ttp-110) cc_final: 0.8057 (ttp-110) REVERT: H 81 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8094 (mmm-85) REVERT: H 96 ASP cc_start: 0.8423 (t0) cc_final: 0.8213 (t70) REVERT: H 105 GLN cc_start: 0.8073 (pm20) cc_final: 0.7767 (pm20) REVERT: L 27 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.8213 (mtt180) REVERT: L 45 LYS cc_start: 0.7849 (tttm) cc_final: 0.7428 (pttp) REVERT: L 79 GLN cc_start: 0.7019 (mm-40) cc_final: 0.6730 (mm110) REVERT: A 138 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: A 289 CYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8632 (m) REVERT: A 416 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8216 (mttp) REVERT: A 420 CYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7536 (p) REVERT: E 6 GLU cc_start: 0.6784 (mp0) cc_final: 0.6518 (mp0) REVERT: E 66 ARG cc_start: 0.8439 (ttp-110) cc_final: 0.8069 (ttp-110) REVERT: E 81 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.8104 (mmm-85) REVERT: E 105 GLN cc_start: 0.8072 (pm20) cc_final: 0.7764 (pm20) REVERT: I 45 LYS cc_start: 0.7873 (tttm) cc_final: 0.7459 (pttp) REVERT: I 61 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7576 (mtm110) REVERT: I 79 GLN cc_start: 0.6937 (mm-40) cc_final: 0.6616 (mm110) REVERT: B 138 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: B 289 CYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8648 (m) REVERT: B 416 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8212 (mttp) REVERT: B 420 CYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7547 (p) REVERT: F 6 GLU cc_start: 0.6792 (mp0) cc_final: 0.6533 (mp0) REVERT: F 66 ARG cc_start: 0.8438 (ttp-110) cc_final: 0.8071 (ttp-110) REVERT: F 81 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8099 (mmm-85) REVERT: F 96 ASP cc_start: 0.8424 (t70) cc_final: 0.8201 (t70) REVERT: F 105 GLN cc_start: 0.8063 (pm20) cc_final: 0.7754 (pm20) REVERT: J 27 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8223 (mtt180) REVERT: J 45 LYS cc_start: 0.7862 (tttm) cc_final: 0.7443 (pttp) REVERT: J 79 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6669 (mm110) REVERT: C 138 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: C 289 CYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8651 (m) REVERT: C 416 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8211 (mttp) REVERT: C 420 CYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7533 (p) REVERT: G 6 GLU cc_start: 0.6780 (mp0) cc_final: 0.6518 (mp0) REVERT: G 66 ARG cc_start: 0.8430 (ttp-110) cc_final: 0.8056 (ttp-110) REVERT: G 81 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8106 (mmm-85) REVERT: G 105 GLN cc_start: 0.8070 (pm20) cc_final: 0.7761 (pm20) REVERT: K 24 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7748 (mmm-85) REVERT: K 45 LYS cc_start: 0.7909 (tttm) cc_final: 0.7513 (pttp) REVERT: K 79 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6745 (mm110) REVERT: D 138 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: D 289 CYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8646 (m) REVERT: D 416 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8215 (mttp) REVERT: D 420 CYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7543 (p) outliers start: 63 outliers final: 42 residues processed: 406 average time/residue: 0.5350 time to fit residues: 246.9387 Evaluate side-chains 423 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 365 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 5 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 289 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 22 THR 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 289 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain J residue 5 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 138 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 289 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain K residue 5 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 289 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 126 optimal weight: 0.9990 chunk 185 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 chunk 173 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.140554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104682 restraints weight = 25787.228| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.36 r_work: 0.3337 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19980 Z= 0.163 Angle : 0.666 12.438 27092 Z= 0.341 Chirality : 0.046 0.140 2908 Planarity : 0.005 0.088 3456 Dihedral : 5.897 58.796 3080 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.47 % Favored : 96.37 % Rotamer: Outliers : 2.71 % Allowed : 25.68 % Favored : 71.62 % 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 (0.17), residues: 2476 helix: None (None), residues: 0 sheet: -0.23 (0.17), residues: 980 loop : -1.03 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 56 TYR 0.012 0.002 TYR H 50 PHE 0.019 0.002 PHE E 78 TRP 0.015 0.001 TRP A 177 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00375 (19964) covalent geometry : angle 0.65571 (27044) hydrogen bonds : bond 0.03470 ( 616) hydrogen bonds : angle 6.08427 ( 1740) link_BETA1-4 : bond 0.00292 ( 8) link_BETA1-4 : angle 2.16639 ( 24) link_NAG-ASN : bond 0.00487 ( 8) link_NAG-ASN : angle 3.37117 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8440.91 seconds wall clock time: 144 minutes 51.06 seconds (8691.06 seconds total)