Starting phenix.real_space_refine on Sat Jul 4 09:57:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyh_46044/07_2026/9cyh_46044.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyh_46044/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cyh_46044/07_2026/9cyh_46044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyh_46044/07_2026/9cyh_46044.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cyh_46044/07_2026/9cyh_46044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyh_46044/07_2026/9cyh_46044.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19488 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3016 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 371} Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "I" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 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: 3.24, per 1000 atoms: 0.17 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: 1.45 Conformation dependent library (CDL) restraints added in 769.7 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: 0.62 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: 3.36 Time building geometry restraints manager: 2.02 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.880 Find NCS groups from input model: 0.470 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:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 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/Z covalent geometry : bond 0.00549 / 0.23 (19964) covalent geometry : angle 0.91927 / 0.47 (27044) hydrogen bonds : bond 0.25967 / 17.19 ( 616) hydrogen bonds : angle 10.57105 / 7.43 ( 1740) link_BETA1-4 : bond 0.00114 / 0.07 ( 8) link_BETA1-4 : angle 3.01023 / 2.61 ( 24) link_NAG-ASN : bond 0.00708 / 0.35 ( 8) link_NAG-ASN : angle 6.37134 / 4.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 516 time to evaluate : 0.838 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 528 average time/residue: 0.5889 time to fit residues: 354.5101 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 : 0.847 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 16 GLN H 40 HIS A 294 ASN A 431 HIS E 16 GLN E 40 HIS B 294 ASN B 431 HIS F 16 GLN F 40 HIS C 294 ASN C 431 HIS G 16 GLN G 40 HIS D 294 ASN D 431 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.141882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.104819 restraints weight = 25125.539| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.45 r_work: 0.3333 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1816 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= 0.175 Angle : 0.691 8.343 27092 Z= 0.355 Chirality : 0.048 0.145 2908 Planarity : 0.005 0.043 3456 Dihedral : 7.293 59.085 3088 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.98 % Allowed : 19.49 % Favored : 75.53 % 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: -1.42 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.33 (0.17), residues: 992 loop : -1.41 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 81 TYR 0.015 0.002 TYR F 100D PHE 0.016 0.002 PHE F 78 TRP 0.013 0.001 TRP A 177 HIS 0.007 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (19964) covalent geometry : angle 0.66832 / 0.35 (27044) hydrogen bonds : bond 0.04960 / 3.27 ( 616) hydrogen bonds : angle 6.99421 / 4.93 ( 1740) link_BETA1-4 : bond 0.00400 / 0.23 ( 8) link_BETA1-4 : angle 2.47849 / 2.08 ( 24) link_NAG-ASN : bond 0.00655 / 0.36 ( 8) link_NAG-ASN : angle 5.38785 / 3.83 ( 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 542 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 439 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.8695 (tttp) cc_final: 0.8371 (mmmt) REVERT: H 81 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.7903 (mmm-85) REVERT: H 102 VAL cc_start: 0.8319 (p) cc_final: 0.8110 (m) REVERT: H 105 GLN cc_start: 0.7246 (pm20) cc_final: 0.6833 (pm20) REVERT: L 24 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7552 (mmm-85) REVERT: L 39 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7731 (mmtm) REVERT: L 42 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7725 (ptpt) REVERT: A 90 SER cc_start: 0.8381 (t) cc_final: 0.7974 (p) REVERT: A 337 CYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8525 (m) REVERT: E 13 LYS cc_start: 0.8696 (tttp) cc_final: 0.8372 (mmmt) REVERT: E 81 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.7899 (mmm-85) REVERT: E 102 VAL cc_start: 0.8327 (p) cc_final: 0.8122 (m) REVERT: E 105 GLN cc_start: 0.7248 (pm20) cc_final: 0.6832 (pm20) REVERT: I 24 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7561 (mmm-85) REVERT: I 39 LYS cc_start: 0.8005 (mmtm) cc_final: 0.7750 (mmtm) REVERT: I 42 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7725 (ptpt) REVERT: B 90 SER cc_start: 0.8376 (t) cc_final: 0.7969 (p) REVERT: B 337 CYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8520 (m) REVERT: F 13 LYS cc_start: 0.8695 (tttp) cc_final: 0.8371 (mmmt) REVERT: F 81 ARG cc_start: 0.8649 (mmm-85) cc_final: 0.7896 (mmm-85) REVERT: F 102 VAL cc_start: 0.8323 (p) cc_final: 0.8118 (m) REVERT: F 105 GLN cc_start: 0.7247 (pm20) cc_final: 0.6833 (pm20) REVERT: J 24 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7549 (mmm-85) REVERT: J 39 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7744 (mmtm) REVERT: J 42 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7726 (ptpt) REVERT: C 90 SER cc_start: 0.8377 (t) cc_final: 0.7972 (p) REVERT: C 337 CYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8520 (m) REVERT: G 13 LYS cc_start: 0.8697 (tttp) cc_final: 0.8371 (mmmt) REVERT: G 81 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.7895 (mmm-85) REVERT: G 102 VAL cc_start: 0.8324 (p) cc_final: 0.8113 (m) REVERT: G 105 GLN cc_start: 0.7250 (pm20) cc_final: 0.6836 (pm20) REVERT: K 24 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7543 (mmm-85) REVERT: K 39 LYS cc_start: 0.7964 (mmtm) cc_final: 0.7728 (mmtm) REVERT: K 42 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7729 (ptpt) REVERT: D 90 SER cc_start: 0.8377 (t) cc_final: 0.7972 (p) REVERT: D 337 CYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8527 (m) REVERT: D 377 MET cc_start: 0.8128 (tpp) cc_final: 0.7828 (tpp) outliers start: 103 outliers final: 44 residues processed: 471 average time/residue: 0.5662 time to fit residues: 305.9247 Evaluate side-chains 473 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 425 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 121 optimal weight: 0.0040 chunk 226 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS B 183 HIS C 183 HIS D 183 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.139230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101125 restraints weight = 25625.780| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.49 r_work: 0.3291 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19980 Z= 0.222 Angle : 0.663 7.541 27092 Z= 0.346 Chirality : 0.047 0.158 2908 Planarity : 0.005 0.041 3456 Dihedral : 6.712 59.519 3080 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 4.93 % Allowed : 20.60 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.35 (0.17), residues: 952 loop : -1.21 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 56 TYR 0.012 0.002 TYR G 50 PHE 0.020 0.002 PHE G 78 TRP 0.013 0.001 TRP A 177 HIS 0.007 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (19964) covalent geometry : angle 0.64899 / 0.34 (27044) hydrogen bonds : bond 0.04165 / 2.75 ( 616) hydrogen bonds : angle 6.40803 / 4.51 ( 1740) link_BETA1-4 : bond 0.00252 / 0.14 ( 8) link_BETA1-4 : angle 2.32493 / 1.91 ( 24) link_NAG-ASN : bond 0.00508 / 0.30 ( 8) link_NAG-ASN : angle 4.10669 / 2.59 ( 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 520 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 418 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6204 (mp0) cc_final: 0.5994 (mp0) REVERT: H 13 LYS cc_start: 0.8690 (tttp) cc_final: 0.8359 (mmmt) REVERT: H 66 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.8000 (ttm170) REVERT: H 81 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8288 (mmm-85) REVERT: H 102 VAL cc_start: 0.8351 (p) cc_final: 0.8150 (m) REVERT: H 105 GLN cc_start: 0.7539 (pm20) cc_final: 0.7066 (pm20) REVERT: L 24 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7700 (mmm-85) REVERT: L 79 GLN cc_start: 0.7121 (mm-40) cc_final: 0.6815 (mm110) REVERT: A 138 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: A 337 CYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8586 (m) REVERT: A 377 MET cc_start: 0.8182 (tpp) cc_final: 0.7902 (tpp) REVERT: A 416 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8187 (mttp) REVERT: E 6 GLU cc_start: 0.6231 (mp0) cc_final: 0.6019 (mp0) REVERT: E 13 LYS cc_start: 0.8693 (tttp) cc_final: 0.8360 (mmmt) REVERT: E 66 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8004 (ttm170) REVERT: E 81 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8289 (mmm-85) REVERT: E 102 VAL cc_start: 0.8374 (p) cc_final: 0.8168 (m) REVERT: E 105 GLN cc_start: 0.7541 (pm20) cc_final: 0.7062 (pm20) REVERT: I 24 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7701 (mmm-85) REVERT: I 79 GLN cc_start: 0.7094 (mm-40) cc_final: 0.6792 (mm110) REVERT: B 138 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: B 337 CYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8584 (m) REVERT: B 416 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8182 (mttp) REVERT: F 6 GLU cc_start: 0.6247 (mp0) cc_final: 0.6035 (mp0) REVERT: F 13 LYS cc_start: 0.8694 (tttp) cc_final: 0.8360 (mmmt) REVERT: F 66 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.8011 (ttm170) REVERT: F 81 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8292 (mmm-85) REVERT: F 102 VAL cc_start: 0.8370 (p) cc_final: 0.8166 (m) REVERT: F 105 GLN cc_start: 0.7558 (pm20) cc_final: 0.7082 (pm20) REVERT: J 24 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7712 (mmm-85) REVERT: J 79 GLN cc_start: 0.7096 (mm-40) cc_final: 0.6796 (mm110) REVERT: C 138 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: C 337 CYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8584 (m) REVERT: C 377 MET cc_start: 0.8193 (tpp) cc_final: 0.7914 (tpp) REVERT: C 416 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8182 (mttp) REVERT: G 6 GLU cc_start: 0.6238 (mp0) cc_final: 0.6027 (mp0) REVERT: G 13 LYS cc_start: 0.8691 (tttp) cc_final: 0.8359 (mmmt) REVERT: G 66 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8006 (ttm170) REVERT: G 81 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8292 (mmm-85) REVERT: G 102 VAL cc_start: 0.8359 (p) cc_final: 0.8158 (m) REVERT: G 105 GLN cc_start: 0.7535 (pm20) cc_final: 0.7056 (pm20) REVERT: K 24 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7701 (mmm-85) REVERT: D 138 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: D 337 CYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8586 (m) REVERT: D 377 MET cc_start: 0.8224 (tpp) cc_final: 0.8019 (tpp) REVERT: D 416 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8181 (mttp) outliers start: 102 outliers final: 63 residues processed: 463 average time/residue: 0.5892 time to fit residues: 310.8018 Evaluate side-chains 468 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 393 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 85 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 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 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 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 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 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 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 K residue 103 LYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 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: 2.9990 chunk 217 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.138387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.101617 restraints weight = 25822.406| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.41 r_work: 0.3302 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 19980 Z= 0.253 Angle : 0.675 8.166 27092 Z= 0.351 Chirality : 0.048 0.149 2908 Planarity : 0.005 0.042 3456 Dihedral : 6.438 59.054 3080 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.04 % Favored : 95.80 % Rotamer: Outliers : 5.27 % Allowed : 21.03 % Favored : 73.69 % 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: -1.27 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.33 (0.17), residues: 916 loop : -1.18 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 56 TYR 0.012 0.002 TYR H 100D PHE 0.020 0.002 PHE H 78 TRP 0.012 0.001 TRP D 177 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.25 (19964) covalent geometry : angle 0.66267 / 0.35 (27044) hydrogen bonds : bond 0.03998 / 2.65 ( 616) hydrogen bonds : angle 6.33836 / 4.45 ( 1740) link_BETA1-4 : bond 0.00227 / 0.13 ( 8) link_BETA1-4 : angle 2.29294 / 1.88 ( 24) link_NAG-ASN : bond 0.00457 / 0.27 ( 8) link_NAG-ASN : angle 3.72536 / 2.15 ( 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 519 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 410 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.8704 (tttp) cc_final: 0.8403 (mmpt) REVERT: H 66 ARG cc_start: 0.8410 (ttp-110) cc_final: 0.7983 (ttm170) REVERT: H 81 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8181 (mmm-85) REVERT: H 96 ASP cc_start: 0.8489 (t70) cc_final: 0.8182 (t70) REVERT: H 102 VAL cc_start: 0.8528 (p) cc_final: 0.8293 (m) REVERT: H 105 GLN cc_start: 0.7620 (pm20) cc_final: 0.7093 (pm20) REVERT: L 24 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7876 (mmm-85) REVERT: L 79 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6722 (mm110) REVERT: A 138 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: A 337 CYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8722 (m) REVERT: A 377 MET cc_start: 0.8414 (tpp) cc_final: 0.8182 (tpp) REVERT: A 416 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8211 (mttp) REVERT: E 13 LYS cc_start: 0.8703 (tttp) cc_final: 0.8402 (mmpt) REVERT: E 66 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.7996 (ttm170) REVERT: E 81 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8190 (mmm-85) REVERT: E 96 ASP cc_start: 0.8483 (t70) cc_final: 0.8216 (t70) REVERT: E 102 VAL cc_start: 0.8550 (p) cc_final: 0.8314 (m) REVERT: E 105 GLN cc_start: 0.7624 (pm20) cc_final: 0.7150 (pm20) REVERT: I 24 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7886 (mmm-85) REVERT: I 79 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6720 (mm110) REVERT: B 138 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: B 337 CYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8727 (m) REVERT: B 416 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8214 (mttp) REVERT: F 13 LYS cc_start: 0.8705 (tttp) cc_final: 0.8403 (mmpt) REVERT: F 66 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.7996 (ttm170) REVERT: F 81 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8182 (mmm-85) REVERT: F 96 ASP cc_start: 0.8492 (t70) cc_final: 0.8186 (t70) REVERT: F 102 VAL cc_start: 0.8551 (p) cc_final: 0.8318 (m) REVERT: F 105 GLN cc_start: 0.7617 (pm20) cc_final: 0.7089 (pm20) REVERT: J 24 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7888 (mmm-85) REVERT: J 79 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6719 (mm110) REVERT: C 138 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: C 337 CYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8729 (m) REVERT: C 377 MET cc_start: 0.8414 (tpp) cc_final: 0.8181 (tpp) REVERT: C 416 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8217 (mttp) REVERT: G 13 LYS cc_start: 0.8703 (tttp) cc_final: 0.8401 (mmpt) REVERT: G 66 ARG cc_start: 0.8416 (ttp-110) cc_final: 0.7990 (ttm170) REVERT: G 81 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8186 (mmm-85) REVERT: G 96 ASP cc_start: 0.8483 (t70) cc_final: 0.8172 (t70) REVERT: G 102 VAL cc_start: 0.8496 (p) cc_final: 0.8257 (m) REVERT: G 105 GLN cc_start: 0.7620 (pm20) cc_final: 0.7146 (pm20) REVERT: K 24 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7882 (mmm-85) REVERT: D 138 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: D 337 CYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8720 (m) REVERT: D 377 MET cc_start: 0.8402 (tpp) cc_final: 0.8148 (tpp) REVERT: D 416 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8221 (mttp) outliers start: 109 outliers final: 69 residues processed: 446 average time/residue: 0.5579 time to fit residues: 284.1212 Evaluate side-chains 478 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 397 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 L residue 103 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 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 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 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 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 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 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 22 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 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 Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 201 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 153 optimal weight: 0.4980 chunk 213 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104675 restraints weight = 25972.932| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.37 r_work: 0.3329 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19980 Z= 0.181 Angle : 0.632 7.373 27092 Z= 0.328 Chirality : 0.046 0.148 2908 Planarity : 0.004 0.048 3456 Dihedral : 6.021 58.559 3080 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.28 % Rotamer: Outliers : 5.22 % Allowed : 22.10 % Favored : 72.68 % 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: -1.13 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.27 (0.17), residues: 940 loop : -1.06 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 56 TYR 0.013 0.001 TYR F 100D PHE 0.019 0.002 PHE G 78 TRP 0.012 0.001 TRP A 177 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (19964) covalent geometry : angle 0.62048 / 0.33 (27044) hydrogen bonds : bond 0.03638 / 2.41 ( 616) hydrogen bonds : angle 6.11139 / 4.29 ( 1740) link_BETA1-4 : bond 0.00268 / 0.15 ( 8) link_BETA1-4 : angle 2.32134 / 1.92 ( 24) link_NAG-ASN : bond 0.00504 / 0.30 ( 8) link_NAG-ASN : angle 3.50705 / 1.96 ( 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 515 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 407 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.8699 (tttp) cc_final: 0.8363 (mmmt) REVERT: H 66 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.8041 (ttm170) REVERT: H 81 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8123 (mmm-85) REVERT: H 105 GLN cc_start: 0.7915 (pm20) cc_final: 0.7461 (pm20) REVERT: L 24 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7790 (mmm-85) REVERT: L 79 GLN cc_start: 0.7091 (mm-40) cc_final: 0.6811 (mm110) REVERT: A 138 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: A 377 MET cc_start: 0.8349 (tpp) cc_final: 0.8095 (tpp) REVERT: A 416 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8148 (mttp) REVERT: A 420 CYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7450 (p) REVERT: E 13 LYS cc_start: 0.8698 (tttp) cc_final: 0.8360 (mmmt) REVERT: E 18 LEU cc_start: 0.7478 (tp) cc_final: 0.7233 (tp) REVERT: E 66 ARG cc_start: 0.8405 (ttp-110) cc_final: 0.8048 (ttm170) REVERT: E 81 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8124 (mmm-85) REVERT: E 105 GLN cc_start: 0.7836 (pm20) cc_final: 0.7386 (pm20) REVERT: I 24 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7803 (mmm-85) REVERT: I 79 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6818 (mm110) REVERT: B 138 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: B 416 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8152 (mttp) REVERT: B 420 CYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7457 (p) REVERT: F 13 LYS cc_start: 0.8700 (tttp) cc_final: 0.8363 (mmmt) REVERT: F 18 LEU cc_start: 0.7481 (tp) cc_final: 0.7238 (tp) REVERT: F 66 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.8050 (ttm170) REVERT: F 81 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8117 (mmm-85) REVERT: F 105 GLN cc_start: 0.7921 (pm20) cc_final: 0.7466 (pm20) REVERT: J 24 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7800 (mmm-85) REVERT: J 79 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6834 (mm110) REVERT: C 138 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: C 377 MET cc_start: 0.8351 (tpp) cc_final: 0.8094 (tpp) REVERT: C 416 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8154 (mttp) REVERT: C 420 CYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7449 (p) REVERT: G 13 LYS cc_start: 0.8697 (tttp) cc_final: 0.8361 (mmmt) REVERT: G 18 LEU cc_start: 0.7487 (tp) cc_final: 0.7237 (tp) REVERT: G 66 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.8042 (ttm170) REVERT: G 81 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8115 (mmm-85) REVERT: G 105 GLN cc_start: 0.7838 (pm20) cc_final: 0.7384 (pm20) REVERT: K 24 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7791 (mmm-85) REVERT: D 138 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: D 416 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8163 (mttp) REVERT: D 420 CYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7465 (p) outliers start: 108 outliers final: 60 residues processed: 444 average time/residue: 0.5461 time to fit residues: 277.6094 Evaluate side-chains 472 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 400 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 VAL 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 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 E residue 52 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain I residue 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 F residue 52 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 102 VAL 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 G residue 52 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 102 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 133 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103480 restraints weight = 25600.864| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.37 r_work: 0.3325 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19980 Z= 0.193 Angle : 0.645 8.059 27092 Z= 0.334 Chirality : 0.046 0.144 2908 Planarity : 0.005 0.059 3456 Dihedral : 5.880 58.908 3080 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 4.64 % Allowed : 22.58 % 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: -1.08 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.19 (0.17), residues: 976 loop : -1.08 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 56 TYR 0.014 0.002 TYR H 100D PHE 0.020 0.002 PHE H 78 TRP 0.011 0.001 TRP B 177 HIS 0.007 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (19964) covalent geometry : angle 0.63383 / 0.33 (27044) hydrogen bonds : bond 0.03552 / 2.36 ( 616) hydrogen bonds : angle 6.03410 / 4.24 ( 1740) link_BETA1-4 : bond 0.00276 / 0.16 ( 8) link_BETA1-4 : angle 2.30607 / 1.90 ( 24) link_NAG-ASN : bond 0.00502 / 0.30 ( 8) link_NAG-ASN : angle 3.44358 / 1.90 ( 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 482 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 386 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6824 (mp0) cc_final: 0.6610 (mp0) REVERT: H 18 LEU cc_start: 0.7518 (tp) cc_final: 0.7289 (tp) REVERT: H 66 ARG cc_start: 0.8378 (ttp-110) cc_final: 0.7977 (ttm170) REVERT: H 81 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8143 (mmm-85) REVERT: H 105 GLN cc_start: 0.7997 (pm20) cc_final: 0.7723 (pm20) REVERT: L 24 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7801 (mmm-85) REVERT: L 27 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8133 (mtt180) REVERT: L 79 GLN cc_start: 0.7076 (mm-40) cc_final: 0.6793 (mm110) REVERT: A 138 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: A 289 CYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8597 (m) REVERT: A 377 MET cc_start: 0.8327 (tpp) cc_final: 0.8110 (tpp) REVERT: A 416 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8151 (mttp) REVERT: A 420 CYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7389 (p) REVERT: E 6 GLU cc_start: 0.6764 (mp0) cc_final: 0.6508 (mp0) REVERT: E 18 LEU cc_start: 0.7507 (tp) cc_final: 0.7282 (tp) REVERT: E 66 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.8007 (ttm170) REVERT: E 81 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8125 (mmm-85) REVERT: E 105 GLN cc_start: 0.7978 (pm20) cc_final: 0.7590 (pm20) REVERT: I 24 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7813 (mmm-85) REVERT: I 27 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8115 (mtt180) REVERT: I 79 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6780 (mm110) REVERT: B 138 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: B 289 CYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8597 (m) REVERT: B 416 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8154 (mttp) REVERT: B 420 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7399 (p) REVERT: F 6 GLU cc_start: 0.6822 (mp0) cc_final: 0.6607 (mp0) REVERT: F 18 LEU cc_start: 0.7502 (tp) cc_final: 0.7272 (tp) REVERT: F 66 ARG cc_start: 0.8408 (ttp-110) cc_final: 0.8009 (ttm170) REVERT: F 81 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8124 (mmm-85) REVERT: F 102 VAL cc_start: 0.8446 (p) cc_final: 0.8213 (m) REVERT: F 105 GLN cc_start: 0.8017 (pm20) cc_final: 0.7736 (pm20) REVERT: J 24 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7811 (mmm-85) REVERT: J 27 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8131 (mtt180) REVERT: J 79 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6835 (mm110) REVERT: C 138 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: C 289 CYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8595 (m) REVERT: C 377 MET cc_start: 0.8327 (tpp) cc_final: 0.8107 (tpp) REVERT: C 416 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8152 (mttp) REVERT: C 420 CYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7393 (p) REVERT: G 6 GLU cc_start: 0.6747 (mp0) cc_final: 0.6492 (mp0) REVERT: G 18 LEU cc_start: 0.7502 (tp) cc_final: 0.7271 (tp) REVERT: G 66 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.8008 (ttm170) REVERT: G 81 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.8120 (mmm-85) REVERT: G 105 GLN cc_start: 0.7973 (pm20) cc_final: 0.7585 (pm20) REVERT: K 24 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7803 (mmm-85) REVERT: K 27 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8120 (mtt180) REVERT: D 138 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: D 289 CYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8603 (m) REVERT: D 416 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8159 (mttp) REVERT: D 420 CYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7408 (p) outliers start: 96 outliers final: 55 residues processed: 438 average time/residue: 0.5167 time to fit residues: 260.1254 Evaluate side-chains 438 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 367 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE 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 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 E residue 52 LEU Chi-restraints excluded: chain E residue 102 VAL 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 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 F residue 52 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain J residue 21 ILE 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 G residue 102 VAL 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 139 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.138395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102079 restraints weight = 25819.336| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.37 r_work: 0.3302 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 19980 Z= 0.242 Angle : 0.668 9.188 27092 Z= 0.346 Chirality : 0.047 0.142 2908 Planarity : 0.005 0.064 3456 Dihedral : 5.928 58.590 3080 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.16 % Favored : 95.68 % Rotamer: Outliers : 5.27 % Allowed : 22.87 % Favored : 71.86 % 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: -0.26 (0.17), residues: 980 loop : -1.07 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 56 TYR 0.014 0.002 TYR F 100D PHE 0.020 0.002 PHE E 78 TRP 0.012 0.001 TRP B 177 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (19964) covalent geometry : angle 0.65720 / 0.34 (27044) hydrogen bonds : bond 0.03704 / 2.46 ( 616) hydrogen bonds : angle 6.06905 / 4.26 ( 1740) link_BETA1-4 : bond 0.00266 / 0.15 ( 8) link_BETA1-4 : angle 2.25089 / 1.82 ( 24) link_NAG-ASN : bond 0.00465 / 0.28 ( 8) link_NAG-ASN : angle 3.46262 / 1.89 ( 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 491 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 382 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.7542 (tp) cc_final: 0.7311 (tp) REVERT: H 66 ARG cc_start: 0.8429 (ttp-110) cc_final: 0.8025 (ttm170) REVERT: H 81 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.8121 (mmm-85) REVERT: H 96 ASP cc_start: 0.8395 (t70) cc_final: 0.8154 (t70) REVERT: H 105 GLN cc_start: 0.8011 (pm20) cc_final: 0.7705 (pm20) REVERT: L 24 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7779 (mmm-85) REVERT: L 27 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.8073 (mtt180) REVERT: L 45 LYS cc_start: 0.7865 (tttm) cc_final: 0.7467 (pttp) REVERT: L 79 GLN cc_start: 0.6994 (mm-40) cc_final: 0.6699 (mm110) REVERT: A 138 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: A 289 CYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8645 (m) REVERT: A 377 MET cc_start: 0.8329 (tpp) cc_final: 0.8016 (tpp) REVERT: A 416 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8172 (mttp) REVERT: A 420 CYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7430 (p) REVERT: E 18 LEU cc_start: 0.7525 (tp) cc_final: 0.7304 (tp) REVERT: E 66 ARG cc_start: 0.8435 (ttp-110) cc_final: 0.8034 (ttm170) REVERT: E 81 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8127 (mmm-85) REVERT: E 96 ASP cc_start: 0.8391 (t70) cc_final: 0.8151 (t70) REVERT: E 105 GLN cc_start: 0.7969 (pm20) cc_final: 0.7671 (pm20) REVERT: I 24 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7782 (mmm-85) REVERT: I 27 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.8049 (mtt180) REVERT: I 39 LYS cc_start: 0.7989 (mmtm) cc_final: 0.7785 (mmtm) REVERT: I 45 LYS cc_start: 0.7865 (tttm) cc_final: 0.7478 (pttp) REVERT: I 79 GLN cc_start: 0.6987 (mm-40) cc_final: 0.6694 (mm110) REVERT: B 138 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: B 289 CYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8640 (m) REVERT: B 416 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8172 (mttp) REVERT: B 420 CYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7449 (p) REVERT: F 6 GLU cc_start: 0.6776 (mp0) cc_final: 0.6569 (mp0) REVERT: F 18 LEU cc_start: 0.7526 (tp) cc_final: 0.7301 (tp) REVERT: F 66 ARG cc_start: 0.8440 (ttp-110) cc_final: 0.8041 (ttm170) REVERT: F 81 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8117 (mmm-85) REVERT: F 96 ASP cc_start: 0.8386 (t70) cc_final: 0.8145 (t70) REVERT: F 102 VAL cc_start: 0.8429 (p) cc_final: 0.8188 (m) REVERT: F 105 GLN cc_start: 0.7999 (pm20) cc_final: 0.7691 (pm20) REVERT: J 24 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7794 (mmm-85) REVERT: J 27 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8062 (mtt180) REVERT: J 45 LYS cc_start: 0.7865 (tttm) cc_final: 0.7462 (pttp) REVERT: J 79 GLN cc_start: 0.7021 (mm-40) cc_final: 0.6812 (mm110) REVERT: C 138 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: C 289 CYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8641 (m) REVERT: C 377 MET cc_start: 0.8331 (tpp) cc_final: 0.8017 (tpp) REVERT: C 416 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8172 (mttp) REVERT: C 420 CYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7446 (p) REVERT: G 18 LEU cc_start: 0.7529 (tp) cc_final: 0.7312 (tp) REVERT: G 66 ARG cc_start: 0.8437 (ttp-110) cc_final: 0.8036 (ttm170) REVERT: G 81 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8112 (mmm-85) REVERT: G 105 GLN cc_start: 0.7987 (pm20) cc_final: 0.7693 (pm20) REVERT: K 24 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7775 (mmm-85) REVERT: K 27 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8032 (mtt180) REVERT: K 45 LYS cc_start: 0.7879 (tttm) cc_final: 0.7490 (pttp) REVERT: D 138 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: D 289 CYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8640 (m) REVERT: D 416 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8180 (mttp) REVERT: D 420 CYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7457 (p) outliers start: 109 outliers final: 68 residues processed: 433 average time/residue: 0.5323 time to fit residues: 264.0798 Evaluate side-chains 453 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 369 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 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 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 102 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 ILE 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 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 F residue 110 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE 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 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 G residue 52 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 ILE 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 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: 3.9990 chunk 149 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 60 ASN E 60 ASN F 60 ASN G 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103497 restraints weight = 25716.227| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.37 r_work: 0.3321 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2846 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= 0.193 Angle : 0.659 10.452 27092 Z= 0.339 Chirality : 0.046 0.140 2908 Planarity : 0.005 0.072 3456 Dihedral : 5.837 58.556 3080 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 4.50 % Allowed : 24.18 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.21 (0.17), residues: 980 loop : -1.04 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 56 TYR 0.013 0.002 TYR G 100D PHE 0.020 0.002 PHE H 78 TRP 0.013 0.001 TRP A 177 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (19964) covalent geometry : angle 0.64860 / 0.34 (27044) hydrogen bonds : bond 0.03533 / 2.34 ( 616) hydrogen bonds : angle 5.99555 / 4.22 ( 1740) link_BETA1-4 : bond 0.00270 / 0.15 ( 8) link_BETA1-4 : angle 2.22166 / 1.80 ( 24) link_NAG-ASN : bond 0.00489 / 0.29 ( 8) link_NAG-ASN : angle 3.38950 / 1.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 372 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6742 (mp0) cc_final: 0.6501 (mp0) REVERT: H 18 LEU cc_start: 0.7564 (tp) cc_final: 0.7349 (tp) REVERT: H 66 ARG cc_start: 0.8388 (ttp-110) cc_final: 0.7904 (ttp-110) REVERT: H 81 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8123 (mmm-85) REVERT: H 96 ASP cc_start: 0.8419 (t70) cc_final: 0.8175 (t70) REVERT: H 105 GLN cc_start: 0.8165 (pm20) cc_final: 0.7868 (pm20) REVERT: L 24 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7809 (mmm-85) REVERT: L 27 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8205 (mtt180) REVERT: L 42 LYS cc_start: 0.8030 (pttp) cc_final: 0.7808 (pmtt) REVERT: L 45 LYS cc_start: 0.7823 (tttm) cc_final: 0.7510 (pttp) REVERT: L 79 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6751 (mm110) REVERT: A 138 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: A 289 CYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8608 (m) REVERT: A 416 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8123 (mttp) REVERT: A 420 CYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7406 (p) REVERT: E 6 GLU cc_start: 0.6705 (mp0) cc_final: 0.6487 (mp0) REVERT: E 18 LEU cc_start: 0.7542 (tp) cc_final: 0.7326 (tp) REVERT: E 66 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.7926 (ttp-110) REVERT: E 81 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8111 (mmm-85) REVERT: E 96 ASP cc_start: 0.8418 (t70) cc_final: 0.8178 (t70) REVERT: E 105 GLN cc_start: 0.8087 (pm20) cc_final: 0.7759 (pm20) REVERT: I 27 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.8186 (mtt180) REVERT: I 42 LYS cc_start: 0.8032 (pttp) cc_final: 0.7802 (pmtt) REVERT: I 45 LYS cc_start: 0.7829 (tttm) cc_final: 0.7414 (pttp) REVERT: I 79 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6843 (mm110) REVERT: B 138 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: B 289 CYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8604 (m) REVERT: B 416 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8120 (mttp) REVERT: B 420 CYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7413 (p) REVERT: F 18 LEU cc_start: 0.7542 (tp) cc_final: 0.7321 (tp) REVERT: F 66 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.7929 (ttp-110) REVERT: F 81 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8107 (mmm-85) REVERT: F 96 ASP cc_start: 0.8329 (t70) cc_final: 0.8070 (t70) REVERT: F 102 VAL cc_start: 0.8411 (p) cc_final: 0.8209 (m) REVERT: F 105 GLN cc_start: 0.8071 (pm20) cc_final: 0.7746 (pm20) REVERT: J 24 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7806 (mmm-85) REVERT: J 27 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8185 (mtt180) REVERT: J 45 LYS cc_start: 0.7823 (tttm) cc_final: 0.7401 (pttp) REVERT: J 79 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6790 (mm110) REVERT: C 138 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: C 289 CYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8608 (m) REVERT: C 416 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8118 (mttp) REVERT: C 420 CYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7414 (p) REVERT: G 6 GLU cc_start: 0.6690 (mp0) cc_final: 0.6474 (mp0) REVERT: G 18 LEU cc_start: 0.7547 (tp) cc_final: 0.7330 (tp) REVERT: G 66 ARG cc_start: 0.8398 (ttp-110) cc_final: 0.7919 (ttp-110) REVERT: G 81 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.8109 (mmm-85) REVERT: G 105 GLN cc_start: 0.8082 (pm20) cc_final: 0.7752 (pm20) REVERT: K 27 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8179 (mtt180) REVERT: K 42 LYS cc_start: 0.8026 (pttp) cc_final: 0.7807 (pmtt) REVERT: K 45 LYS cc_start: 0.7792 (tttm) cc_final: 0.7376 (pttp) REVERT: D 138 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: D 289 CYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8612 (m) REVERT: D 416 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8130 (mttp) REVERT: D 420 CYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7422 (p) outliers start: 93 outliers final: 57 residues processed: 429 average time/residue: 0.4937 time to fit residues: 242.8716 Evaluate side-chains 435 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 362 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 21 ILE 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 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 I residue 5 THR Chi-restraints excluded: chain I residue 21 ILE 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 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 F residue 74 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE 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 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 74 SER Chi-restraints excluded: chain G residue 102 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 138 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 153 optimal weight: 0.0050 chunk 13 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.136227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.099603 restraints weight = 25833.578| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.34 r_work: 0.3268 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 19980 Z= 0.352 Angle : 0.743 10.635 27092 Z= 0.385 Chirality : 0.050 0.149 2908 Planarity : 0.006 0.083 3456 Dihedral : 6.145 58.407 3080 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.64 % Favored : 95.19 % Rotamer: Outliers : 5.13 % Allowed : 23.40 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.35 (0.17), residues: 996 loop : -1.16 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 56 TYR 0.015 0.002 TYR B 383 PHE 0.021 0.002 PHE E 78 TRP 0.013 0.002 TRP A 177 HIS 0.006 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.35 (19964) covalent geometry : angle 0.73267 / 0.38 (27044) hydrogen bonds : bond 0.04041 / 2.68 ( 616) hydrogen bonds : angle 6.23457 / 4.39 ( 1740) link_BETA1-4 : bond 0.00224 / 0.13 ( 8) link_BETA1-4 : angle 2.18842 / 1.72 ( 24) link_NAG-ASN : bond 0.00390 / 0.23 ( 8) link_NAG-ASN : angle 3.57080 / 1.94 ( 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 487 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 381 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6751 (mp0) cc_final: 0.6516 (mp0) REVERT: H 66 ARG cc_start: 0.8463 (ttp-110) cc_final: 0.8187 (ttp-110) REVERT: H 81 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8129 (mmm-85) REVERT: H 96 ASP cc_start: 0.8435 (t70) cc_final: 0.8213 (t70) REVERT: H 105 GLN cc_start: 0.8158 (pm20) cc_final: 0.7907 (pm20) REVERT: L 24 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7813 (mmm-85) REVERT: L 27 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8132 (mtt180) REVERT: L 42 LYS cc_start: 0.8026 (pttp) cc_final: 0.7776 (pmtt) REVERT: L 45 LYS cc_start: 0.7918 (tttm) cc_final: 0.7488 (pttp) REVERT: L 79 GLN cc_start: 0.7051 (mm-40) cc_final: 0.6692 (mm110) REVERT: A 138 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: A 171 ILE cc_start: 0.8451 (mp) cc_final: 0.8221 (mp) REVERT: A 289 CYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8650 (m) REVERT: A 416 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8223 (mttp) REVERT: A 420 CYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7547 (p) REVERT: A 424 CYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8383 (m) REVERT: E 6 GLU cc_start: 0.6700 (mp0) cc_final: 0.6461 (mp0) REVERT: E 66 ARG cc_start: 0.8449 (ttp-110) cc_final: 0.7980 (ttp-110) REVERT: E 81 ARG cc_start: 0.8479 (mmm-85) cc_final: 0.8122 (mmm-85) REVERT: E 96 ASP cc_start: 0.8427 (t70) cc_final: 0.8207 (t70) REVERT: E 105 GLN cc_start: 0.8080 (pm20) cc_final: 0.7783 (pm20) REVERT: I 27 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8184 (mtt180) REVERT: I 42 LYS cc_start: 0.8035 (pttp) cc_final: 0.7781 (pmtt) REVERT: I 45 LYS cc_start: 0.7910 (tttm) cc_final: 0.7539 (pttp) REVERT: I 79 GLN cc_start: 0.7068 (mm-40) cc_final: 0.6642 (mm110) REVERT: B 138 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: B 171 ILE cc_start: 0.8465 (mp) cc_final: 0.8256 (mp) REVERT: B 289 CYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8645 (m) REVERT: B 416 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8224 (mttp) REVERT: B 420 CYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7556 (p) REVERT: B 424 CYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8370 (m) REVERT: F 6 GLU cc_start: 0.6865 (mp0) cc_final: 0.6607 (mp0) REVERT: F 66 ARG cc_start: 0.8455 (ttp-110) cc_final: 0.8187 (ttp-110) REVERT: F 81 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8118 (mmm-85) REVERT: F 96 ASP cc_start: 0.8415 (t70) cc_final: 0.8197 (t70) REVERT: F 105 GLN cc_start: 0.8166 (pm20) cc_final: 0.7911 (pm20) REVERT: J 24 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7824 (mmm-85) REVERT: J 27 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.8132 (mtt180) REVERT: J 45 LYS cc_start: 0.7900 (tttm) cc_final: 0.7515 (pttp) REVERT: J 79 GLN cc_start: 0.7072 (mm-40) cc_final: 0.6779 (mm110) REVERT: C 138 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: C 171 ILE cc_start: 0.8447 (mp) cc_final: 0.8217 (mp) REVERT: C 289 CYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8648 (m) REVERT: C 416 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8242 (mttp) REVERT: C 420 CYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7547 (p) REVERT: G 6 GLU cc_start: 0.6708 (mp0) cc_final: 0.6468 (mp0) REVERT: G 66 ARG cc_start: 0.8448 (ttp-110) cc_final: 0.7976 (ttp-110) REVERT: G 81 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.8125 (mmm-85) REVERT: G 105 GLN cc_start: 0.8069 (pm20) cc_final: 0.7772 (pm20) REVERT: K 27 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8188 (mtt180) REVERT: K 42 LYS cc_start: 0.8023 (pttp) cc_final: 0.7774 (pmtt) REVERT: K 45 LYS cc_start: 0.7931 (tttm) cc_final: 0.7555 (pttp) REVERT: K 79 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6090 (mp10) REVERT: K 82 ASP cc_start: 0.6854 (m-30) cc_final: 0.6613 (m-30) REVERT: D 138 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: D 171 ILE cc_start: 0.8466 (mp) cc_final: 0.8255 (mp) REVERT: D 289 CYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8639 (m) REVERT: D 416 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8260 (mttp) REVERT: D 420 CYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7561 (p) REVERT: D 424 CYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8382 (m) outliers start: 106 outliers final: 63 residues processed: 440 average time/residue: 0.5667 time to fit residues: 285.6556 Evaluate side-chains 454 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 371 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 VAL 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 L residue 103 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 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 424 CYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain 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 424 CYS Chi-restraints excluded: chain B residue 456 TRP 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 51 ILE Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 102 VAL 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 79 GLN Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 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 424 CYS Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 99 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 194 optimal weight: 0.0370 chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 184 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104460 restraints weight = 25456.899| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.40 r_work: 0.3341 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19980 Z= 0.150 Angle : 0.655 11.605 27092 Z= 0.334 Chirality : 0.046 0.141 2908 Planarity : 0.005 0.087 3456 Dihedral : 5.833 58.382 3080 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.57 % Rotamer: Outliers : 3.19 % Allowed : 25.73 % Favored : 71.08 % 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: -1.04 (0.17), residues: 2476 helix: None (None), residues: 0 sheet: -0.23 (0.17), residues: 980 loop : -1.01 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 56 TYR 0.012 0.001 TYR E 50 PHE 0.020 0.002 PHE E 78 TRP 0.014 0.001 TRP B 177 HIS 0.007 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (19964) covalent geometry : angle 0.64449 / 0.33 (27044) hydrogen bonds : bond 0.03399 / 2.26 ( 616) hydrogen bonds : angle 6.01828 / 4.23 ( 1740) link_BETA1-4 : bond 0.00271 / 0.15 ( 8) link_BETA1-4 : angle 2.20037 / 1.79 ( 24) link_NAG-ASN : bond 0.00517 / 0.30 ( 8) link_NAG-ASN : angle 3.33860 / 1.81 ( 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 451 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 385 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.7547 (tp) cc_final: 0.7216 (tp) REVERT: H 66 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.8097 (ttp-110) REVERT: H 81 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8083 (mmm-85) REVERT: H 105 GLN cc_start: 0.8211 (pm20) cc_final: 0.8005 (pm20) REVERT: L 27 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.8220 (mtt180) REVERT: L 45 LYS cc_start: 0.7848 (tttm) cc_final: 0.7392 (pttp) REVERT: L 79 GLN cc_start: 0.7019 (mm-40) cc_final: 0.6741 (mm110) REVERT: A 138 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: A 289 CYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8636 (m) REVERT: A 416 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8123 (mttp) REVERT: A 420 CYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7443 (p) REVERT: E 18 LEU cc_start: 0.7548 (tp) cc_final: 0.7219 (tp) REVERT: E 66 ARG cc_start: 0.8353 (ttp-110) cc_final: 0.8112 (ttp-110) REVERT: E 81 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8078 (mmm-85) REVERT: E 105 GLN cc_start: 0.8117 (pm20) cc_final: 0.7797 (pm20) REVERT: I 27 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8233 (mtt180) REVERT: I 45 LYS cc_start: 0.7870 (tttm) cc_final: 0.7422 (pttp) REVERT: I 79 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6766 (mm110) REVERT: B 90 SER cc_start: 0.8634 (t) cc_final: 0.8369 (m) REVERT: B 138 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: B 289 CYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8633 (m) REVERT: B 416 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8127 (mttp) REVERT: B 420 CYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7452 (p) REVERT: F 18 LEU cc_start: 0.7543 (tp) cc_final: 0.7266 (tp) REVERT: F 66 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.8116 (ttp-110) REVERT: F 81 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8075 (mmm-85) REVERT: F 96 ASP cc_start: 0.8340 (t70) cc_final: 0.8034 (t70) REVERT: F 105 GLN cc_start: 0.8083 (pm20) cc_final: 0.7775 (pm20) REVERT: J 27 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8212 (mtt180) REVERT: J 45 LYS cc_start: 0.7809 (tttm) cc_final: 0.7341 (pttp) REVERT: J 79 GLN cc_start: 0.7068 (mm-40) cc_final: 0.6730 (mm110) REVERT: C 138 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: C 289 CYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8627 (m) REVERT: C 416 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8103 (mttp) REVERT: C 420 CYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7423 (p) REVERT: G 18 LEU cc_start: 0.7550 (tp) cc_final: 0.7270 (tp) REVERT: G 66 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8109 (ttp-110) REVERT: G 81 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8072 (mmm-85) REVERT: G 105 GLN cc_start: 0.8114 (pm20) cc_final: 0.7792 (pm20) REVERT: K 27 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.8217 (mtt180) REVERT: K 45 LYS cc_start: 0.7877 (tttm) cc_final: 0.7426 (pttp) REVERT: K 79 GLN cc_start: 0.6720 (OUTLIER) cc_final: 0.6443 (mm110) REVERT: D 90 SER cc_start: 0.8630 (t) cc_final: 0.8366 (m) REVERT: D 138 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: D 289 CYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8628 (m) REVERT: D 416 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8082 (mttp) REVERT: D 420 CYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7460 (p) outliers start: 66 outliers final: 33 residues processed: 432 average time/residue: 0.5142 time to fit residues: 255.1399 Evaluate side-chains 417 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 367 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU 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 11 LEU Chi-restraints excluded: chain E residue 102 VAL 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 11 LEU Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 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 71 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 79 GLN 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 126 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 157 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN B 225 GLN C 225 GLN D 225 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101871 restraints weight = 25855.599| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.36 r_work: 0.3298 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19980 Z= 0.263 Angle : 0.708 12.161 27092 Z= 0.364 Chirality : 0.048 0.139 2908 Planarity : 0.006 0.086 3456 Dihedral : 5.977 57.908 3080 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 2.51 % Allowed : 26.40 % Favored : 71.08 % 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: -1.15 (0.16), residues: 2476 helix: None (None), residues: 0 sheet: -0.30 (0.17), residues: 980 loop : -1.08 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG K 56 TYR 0.016 0.002 TYR G 100G PHE 0.021 0.002 PHE H 78 TRP 0.013 0.001 TRP C 177 HIS 0.006 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (19964) covalent geometry : angle 0.69834 / 0.36 (27044) hydrogen bonds : bond 0.03791 / 2.50 ( 616) hydrogen bonds : angle 6.18619 / 4.36 ( 1740) link_BETA1-4 : bond 0.00315 / 0.18 ( 8) link_BETA1-4 : angle 2.15256 / 1.68 ( 24) link_NAG-ASN : bond 0.00456 / 0.27 ( 8) link_NAG-ASN : angle 3.43690 / 1.87 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8814.19 seconds wall clock time: 151 minutes 11.05 seconds (9071.05 seconds total)