Starting phenix.real_space_refine on Thu Oct 29 19:28:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afo_11772/10_2026/7afo_11772_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afo_11772/10_2026/7afo_11772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7afo_11772/10_2026/7afo_11772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afo_11772/10_2026/7afo_11772.map" model { file = "/net/cci-nas-00/data/ceres_data/7afo_11772/10_2026/7afo_11772_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afo_11772/10_2026/7afo_11772_neut.cif" } resolution = 3.93 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= 0.004 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: 6 Type Number sf(0) Gaussians P 971 5.49 5 Mg 20 5.21 5 S 59 5.16 5 C 17608 2.51 5 N 6333 2.21 5 O 9143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34134 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 20869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 20869 Classifications: {'RNA': 971} Modifications used: {'rna2p': 2, 'rna2p_pur': 76, 'rna2p_pyr': 52, 'rna3p': 1, 'rna3p_pur': 484, 'rna3p_pyr': 356} Link IDs: {'rna2p': 129, 'rna3p': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1144 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 430 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "Y" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1963 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 19, 'TRANS': 232} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Unusual residues: {' MG': 20} Classifications: {'undetermined': 20} Link IDs: {None: 19} Time building chain proxies: 6.70, per 1000 atoms: 0.20 Number of scatterers: 34134 At special positions: 0 Unit cell: (124.775, 158.41, 218.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 59 16.00 P 971 15.00 Mg 20 11.99 O 9143 8.00 N 6333 7.00 C 17608 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 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 708.2 milliseconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3150 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 15 sheets defined 45.9% alpha, 19.5% beta 339 base pairs and 482 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.955A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 40 through 44 removed outlier: 3.692A pdb=" N ALA D 43 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 152 through 165 removed outlier: 4.215A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 196 through 206 removed outlier: 4.662A pdb=" N LEU D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.959A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 157 through 164 removed outlier: 3.795A pdb=" N VAL E 161 " --> pdb=" O ARG E 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 16 removed outlier: 5.614A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 32 Processing helix chain 'F' and resid 67 through 81 removed outlier: 4.005A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'H' and resid 113 through 120 removed outlier: 3.700A pdb=" N GLN H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 53 through 58 Processing helix chain 'K' and resid 59 through 78 removed outlier: 3.622A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 4.302A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.056A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 4.017A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 49 through 52' Processing helix chain 'R' and resid 11 through 20 removed outlier: 3.731A pdb=" N GLU R 20 " --> pdb=" O GLU R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 Processing helix chain 'R' and resid 31 through 33 No H-bonds generated for 'chain 'R' and resid 31 through 33' Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 41 removed outlier: 3.862A pdb=" N SER T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG T 24 " --> pdb=" O HIS T 20 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS T 34 " --> pdb=" O THR T 30 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 85 Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 27 through 35 Processing helix chain 'U' and resid 40 through 57 removed outlier: 4.188A pdb=" N GLU U 44 " --> pdb=" O LYS U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 61 removed outlier: 3.991A pdb=" N ALA U 61 " --> pdb=" O LYS U 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 58 through 61' Processing helix chain 'X' and resid 4 through 19 Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 47 through 62 Processing helix chain 'X' and resid 63 through 66 Processing helix chain 'X' and resid 87 through 94 removed outlier: 3.540A pdb=" N PHE X 94 " --> pdb=" O HIS X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 132 Processing helix chain 'Y' and resid 22 through 34 removed outlier: 3.523A pdb=" N ASN Y 34 " --> pdb=" O VAL Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 59 removed outlier: 3.762A pdb=" N THR Y 52 " --> pdb=" O LEU Y 48 " (cutoff:3.500A) Proline residue: Y 54 - end of helix Processing helix chain 'Y' and resid 68 through 77 Processing helix chain 'Y' and resid 81 through 83 No H-bonds generated for 'chain 'Y' and resid 81 through 83' Processing helix chain 'Y' and resid 91 through 95 Processing helix chain 'Y' and resid 96 through 104 Processing helix chain 'Y' and resid 118 through 128 Processing helix chain 'Y' and resid 142 through 149 Processing helix chain 'Y' and resid 158 through 167 Processing helix chain 'Y' and resid 177 through 181 Processing helix chain 'Y' and resid 206 through 219 removed outlier: 4.045A pdb=" N LEU Y 210 " --> pdb=" O ASP Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 224 through 232 removed outlier: 5.005A pdb=" N LEU Y 229 " --> pdb=" O ARG Y 226 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY Y 230 " --> pdb=" O ASN Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 234 through 241 Processing helix chain 'Y' and resid 248 through 252 Processing helix chain 'Y' and resid 253 through 268 Processing sheet with id=AA1, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.973A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 12 through 21 removed outlier: 5.149A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY E 51 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'F' and resid 36 through 44 removed outlier: 6.037A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP F 41 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR F 59 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.687A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 65 through 66 Processing sheet with id=AA7, first strand: chain 'H' and resid 75 through 77 Processing sheet with id=AA8, first strand: chain 'H' and resid 75 through 77 removed outlier: 6.644A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.255A pdb=" N ALA K 21 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LYS K 87 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE K 23 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'X' and resid 22 through 30 removed outlier: 4.934A pdb=" N LEU X 23 " --> pdb=" O ASP X 41 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP X 41 " --> pdb=" O LEU X 23 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER X 34 " --> pdb=" O ASN X 73 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLU X 75 " --> pdb=" O SER X 34 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU X 36 " --> pdb=" O GLU X 75 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER X 77 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE X 38 " --> pdb=" O SER X 77 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N TYR L 95 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR L 64 " --> pdb=" O TYR L 95 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR L 97 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TYR L 66 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 50 through 52 removed outlier: 5.749A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 7 through 14 removed outlier: 8.097A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 29 through 30 Processing sheet with id=AB5, first strand: chain 'X' and resid 83 through 84 Processing sheet with id=AB6, first strand: chain 'Y' and resid 85 through 89 removed outlier: 6.816A pdb=" N LEU Y 108 " --> pdb=" O ALA Y 134 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N MET Y 136 " --> pdb=" O LEU Y 108 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL Y 110 " --> pdb=" O MET Y 136 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE Y 138 " --> pdb=" O VAL Y 110 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY Y 112 " --> pdb=" O PHE Y 138 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU Y 140 " --> pdb=" O GLY Y 112 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA Y 134 " --> pdb=" O PRO Y 196 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER Y 189 " --> pdb=" O GLU Y 175 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLU Y 175 " --> pdb=" O SER Y 189 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL Y 191 " --> pdb=" O VAL Y 173 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 851 hydrogen bonds 1342 hydrogen bond angles 0 basepair planarities 339 basepair parallelities 482 stacking parallelities Total time for adding SS restraints: 10.46 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 3107 1.29 - 1.42: 15994 1.42 - 1.56: 15675 1.56 - 1.69: 1940 1.69 - 1.82: 103 Bond restraints: 36819 Sorted by residual: bond pdb=" N9 A A1393 " pdb=" C4 A A1393 " ideal model delta sigma weight residual 1.374 1.334 0.040 6.00e-03 2.78e+04 4.42e+01 bond pdb=" C LEU Y 229 " pdb=" O LEU Y 229 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.29e-02 6.01e+03 4.03e+01 bond pdb=" C5 A A1393 " pdb=" C6 A A1393 " ideal model delta sigma weight residual 1.406 1.354 0.052 9.00e-03 1.23e+04 3.30e+01 bond pdb=" C5 A A 766 " pdb=" C4 A A 766 " ideal model delta sigma weight residual 1.383 1.343 0.040 7.00e-03 2.04e+04 3.22e+01 bond pdb=" C5 A A 915 " pdb=" C4 A A 915 " ideal model delta sigma weight residual 1.383 1.343 0.040 7.00e-03 2.04e+04 3.20e+01 ... (remaining 36814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 46147 2.75 - 5.49: 7780 5.49 - 8.24: 587 8.24 - 10.98: 42 10.98 - 13.73: 6 Bond angle restraints: 54562 Sorted by residual: angle pdb=" C6 A A1393 " pdb=" N1 A A1393 " pdb=" C2 A A1393 " ideal model delta sigma weight residual 118.60 125.73 -7.13 6.00e-01 2.78e+00 1.41e+02 angle pdb=" N6 A A 914 " pdb=" C6 A A 914 " pdb=" N1 A A 914 " ideal model delta sigma weight residual 118.60 111.73 6.87 6.00e-01 2.78e+00 1.31e+02 angle pdb=" N6 A A 621 " pdb=" C6 A A 621 " pdb=" N1 A A 621 " ideal model delta sigma weight residual 118.60 111.75 6.85 6.00e-01 2.78e+00 1.30e+02 angle pdb=" N6 A A 665 " pdb=" C6 A A 665 " pdb=" N1 A A 665 " ideal model delta sigma weight residual 118.60 111.77 6.83 6.00e-01 2.78e+00 1.29e+02 angle pdb=" N6 A A 845 " pdb=" C6 A A 845 " pdb=" N1 A A 845 " ideal model delta sigma weight residual 118.60 111.89 6.71 6.00e-01 2.78e+00 1.25e+02 ... (remaining 54557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 21143 35.90 - 71.81: 2177 71.81 - 107.71: 208 107.71 - 143.62: 16 143.62 - 179.52: 5 Dihedral angle restraints: 23549 sinusoidal: 18678 harmonic: 4871 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 59.40 140.60 1 1.50e+01 4.44e-03 7.56e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 60.09 139.91 1 1.50e+01 4.44e-03 7.53e+01 dihedral pdb=" O4' U A 85 " pdb=" C1' U A 85 " pdb=" N1 U A 85 " pdb=" C2 U A 85 " ideal model delta sinusoidal sigma weight residual 232.00 52.48 179.52 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 23546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 5156 0.100 - 0.199: 1508 0.199 - 0.299: 204 0.299 - 0.399: 22 0.399 - 0.499: 4 Chirality restraints: 6894 Sorted by residual: chirality pdb=" CA TYR Y 116 " pdb=" N TYR Y 116 " pdb=" C TYR Y 116 " pdb=" CB TYR Y 116 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA ARG X 110 " pdb=" N ARG X 110 " pdb=" C ARG X 110 " pdb=" CB ARG X 110 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CA GLN T 55 " pdb=" N GLN T 55 " pdb=" C GLN T 55 " pdb=" CB GLN T 55 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 ... (remaining 6891 not shown) Planarity restraints: 3326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 844 " 0.284 2.00e-02 2.50e+03 1.60e-01 7.71e+02 pdb=" N9 G A 844 " 0.021 2.00e-02 2.50e+03 pdb=" C8 G A 844 " -0.261 2.00e-02 2.50e+03 pdb=" N7 G A 844 " -0.193 2.00e-02 2.50e+03 pdb=" C5 G A 844 " 0.016 2.00e-02 2.50e+03 pdb=" C6 G A 844 " 0.119 2.00e-02 2.50e+03 pdb=" O6 G A 844 " 0.126 2.00e-02 2.50e+03 pdb=" N1 G A 844 " 0.138 2.00e-02 2.50e+03 pdb=" C2 G A 844 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G A 844 " -0.268 2.00e-02 2.50e+03 pdb=" N3 G A 844 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 844 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 346 " 0.306 2.00e-02 2.50e+03 1.39e-01 5.81e+02 pdb=" N9 G A 346 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G A 346 " -0.118 2.00e-02 2.50e+03 pdb=" N7 G A 346 " -0.137 2.00e-02 2.50e+03 pdb=" C5 G A 346 " -0.102 2.00e-02 2.50e+03 pdb=" C6 G A 346 " 0.024 2.00e-02 2.50e+03 pdb=" O6 G A 346 " 0.282 2.00e-02 2.50e+03 pdb=" N1 G A 346 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G A 346 " -0.038 2.00e-02 2.50e+03 pdb=" N2 G A 346 " -0.040 2.00e-02 2.50e+03 pdb=" N3 G A 346 " -0.051 2.00e-02 2.50e+03 pdb=" C4 G A 346 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 845 " 0.310 2.00e-02 2.50e+03 1.42e-01 5.55e+02 pdb=" N9 A A 845 " -0.024 2.00e-02 2.50e+03 pdb=" C8 A A 845 " -0.074 2.00e-02 2.50e+03 pdb=" N7 A A 845 " -0.124 2.00e-02 2.50e+03 pdb=" C5 A A 845 " -0.094 2.00e-02 2.50e+03 pdb=" C6 A A 845 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A A 845 " 0.264 2.00e-02 2.50e+03 pdb=" N1 A A 845 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A 845 " -0.061 2.00e-02 2.50e+03 pdb=" N3 A A 845 " -0.098 2.00e-02 2.50e+03 pdb=" C4 A A 845 " -0.111 2.00e-02 2.50e+03 ... (remaining 3323 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 28 2.47 - 3.07: 22717 3.07 - 3.68: 73246 3.68 - 4.29: 97887 4.29 - 4.90: 133881 Nonbonded interactions: 327759 Sorted by model distance: nonbonded pdb=" OP1 G A 558 " pdb="MG MG A1610 " model vdw 1.857 2.170 nonbonded pdb=" OP2 A A 573 " pdb="MG MG A1614 " model vdw 1.882 2.170 nonbonded pdb=" OP1 G A 21 " pdb="MG MG A1604 " model vdw 1.883 2.170 nonbonded pdb=" OP2 U A 398 " pdb="MG MG A1611 " model vdw 1.891 2.170 nonbonded pdb=" OP1 A A 174 " pdb="MG MG A1609 " model vdw 1.900 2.170 ... (remaining 327754 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 36.730 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 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 : 0.014 0.088 36819 Z= 1.355 Angle : 1.969 13.729 54562 Z= 2.028 Chirality : 0.091 0.499 6894 Planarity : 0.035 0.242 3326 Dihedral : 23.116 179.519 20399 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.71 % Allowed : 8.91 % Favored : 90.38 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.19), residues: 1660 helix: -1.55 (0.17), residues: 690 sheet: -0.31 (0.34), residues: 203 loop : -1.21 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG P 25 TYR 0.210 0.029 TYR Y 157 PHE 0.084 0.013 PHE X 136 TRP 0.088 0.025 TRP X 113 HIS 0.016 0.004 HIS Y 137 Details of bonding type rmsd/Z covalent geometry : bond 0.01394 / 1.36 (36819) covalent geometry : angle 1.96862 / 2.03 (54562) hydrogen bonds : bond 0.12454 / 12.87 ( 1506) hydrogen bonds : angle 8.07035 / 10.46 ( 3181) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 502 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7761 (t80) cc_final: 0.7359 (t80) REVERT: D 51 TYR cc_start: 0.9479 (t80) cc_final: 0.8965 (t80) REVERT: D 71 GLN cc_start: 0.9123 (mt0) cc_final: 0.8827 (mt0) REVERT: D 74 ASN cc_start: 0.9306 (m-40) cc_final: 0.8890 (m-40) REVERT: D 75 TYR cc_start: 0.9308 (m-80) cc_final: 0.8962 (m-80) REVERT: D 76 TYR cc_start: 0.9548 (t80) cc_final: 0.9275 (t80) REVERT: D 77 LYS cc_start: 0.9612 (mtmt) cc_final: 0.9368 (ptpt) REVERT: D 132 ILE cc_start: 0.9305 (mm) cc_final: 0.9053 (mm) REVERT: D 178 MET cc_start: 0.8322 (mtm) cc_final: 0.8081 (mtm) REVERT: D 182 PHE cc_start: 0.9504 (t80) cc_final: 0.9030 (t80) REVERT: D 196 ASN cc_start: 0.8969 (m-40) cc_final: 0.8539 (m110) REVERT: E 30 ILE cc_start: 0.8082 (mm) cc_final: 0.7758 (mm) REVERT: E 54 ARG cc_start: 0.9072 (mmm160) cc_final: 0.8796 (mpt180) REVERT: E 64 MET cc_start: 0.9288 (mmt) cc_final: 0.8874 (mmm) REVERT: E 72 ILE cc_start: 0.9409 (pt) cc_final: 0.9163 (tp) REVERT: E 134 ILE cc_start: 0.9710 (pt) cc_final: 0.9452 (mm) REVERT: E 141 ILE cc_start: 0.9818 (mm) cc_final: 0.9615 (mm) REVERT: E 156 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8538 (mmtt) REVERT: F 6 ILE cc_start: 0.9423 (mt) cc_final: 0.9190 (mm) REVERT: F 8 PHE cc_start: 0.9589 (p90) cc_final: 0.9339 (p90) REVERT: F 62 MET cc_start: 0.8961 (mtp) cc_final: 0.8413 (mpp) REVERT: F 79 ARG cc_start: 0.8858 (ptp90) cc_final: 0.8429 (mpp80) REVERT: F 88 MET cc_start: 0.9026 (ttm) cc_final: 0.8705 (ttm) REVERT: F 90 MET cc_start: 0.8578 (mmm) cc_final: 0.8319 (mmm) REVERT: F 92 THR cc_start: 0.8920 (p) cc_final: 0.8253 (p) REVERT: H 5 ASP cc_start: 0.7893 (t0) cc_final: 0.7310 (t0) REVERT: H 11 LEU cc_start: 0.9795 (mt) cc_final: 0.9494 (mt) REVERT: H 27 MET cc_start: 0.9099 (mpp) cc_final: 0.8632 (mpp) REVERT: H 38 ASN cc_start: 0.9613 (t0) cc_final: 0.8727 (t0) REVERT: H 43 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8707 (tp30) REVERT: H 85 ILE cc_start: 0.9452 (mm) cc_final: 0.9072 (mm) REVERT: H 86 TYR cc_start: 0.8363 (m-80) cc_final: 0.7538 (m-10) REVERT: H 90 ASP cc_start: 0.9645 (p0) cc_final: 0.9430 (p0) REVERT: H 124 GLU cc_start: 0.9043 (tt0) cc_final: 0.8275 (tt0) REVERT: K 33 THR cc_start: 0.8554 (p) cc_final: 0.8061 (p) REVERT: K 125 LYS cc_start: 0.9474 (pttt) cc_final: 0.9185 (ptpp) REVERT: L 5 ASN cc_start: 0.9535 (t0) cc_final: 0.8977 (t0) REVERT: L 35 THR cc_start: 0.9425 (p) cc_final: 0.9064 (p) REVERT: L 55 VAL cc_start: 0.9588 (OUTLIER) cc_final: 0.9372 (p) REVERT: L 73 ASN cc_start: 0.8241 (p0) cc_final: 0.7896 (p0) REVERT: L 103 ASP cc_start: 0.9117 (t0) cc_final: 0.8531 (t0) REVERT: O 68 ASP cc_start: 0.9253 (m-30) cc_final: 0.9046 (m-30) REVERT: P 26 ASN cc_start: 0.9068 (m110) cc_final: 0.8778 (m110) REVERT: Q 38 ILE cc_start: 0.9761 (pt) cc_final: 0.9546 (mm) REVERT: Q 80 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8117 (tm-30) REVERT: R 12 ARG cc_start: 0.6493 (mmp-170) cc_final: 0.6212 (mmp80) REVERT: T 13 GLN cc_start: 0.9509 (pt0) cc_final: 0.9041 (pp30) REVERT: U 23 CYS cc_start: 0.8908 (p) cc_final: 0.8606 (p) REVERT: U 35 ARG cc_start: 0.9051 (ttm170) cc_final: 0.8823 (mtt180) REVERT: U 36 GLU cc_start: 0.9699 (tp30) cc_final: 0.9270 (tp30) REVERT: U 40 LYS cc_start: 0.9605 (mtpt) cc_final: 0.9335 (ttpt) REVERT: X 101 LEU cc_start: 0.9391 (mp) cc_final: 0.8848 (tp) REVERT: Y 136 MET cc_start: 0.8662 (mpt) cc_final: 0.8453 (mpt) REVERT: Y 137 HIS cc_start: 0.8588 (m90) cc_final: 0.8243 (m170) REVERT: Y 159 ARG cc_start: 0.9057 (tmt170) cc_final: 0.8840 (tmm-80) REVERT: Y 163 MET cc_start: 0.9699 (mmm) cc_final: 0.9121 (mmm) REVERT: Y 202 HIS cc_start: 0.9302 (m90) cc_final: 0.9026 (m90) REVERT: Y 241 MET cc_start: 0.9124 (mmm) cc_final: 0.8732 (mmt) REVERT: Y 247 MET cc_start: 0.8947 (mtm) cc_final: 0.8659 (mpp) outliers start: 10 outliers final: 2 residues processed: 508 average time/residue: 0.2679 time to fit residues: 201.5233 Evaluate side-chains 353 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 350 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain Y residue 42 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 258] chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN K 38 GLN K 81 ASN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 HIS T 84 ASN U 56 HIS Y 34 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.025463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.020343 restraints weight = 430605.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.021155 restraints weight = 170542.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.021640 restraints weight = 98242.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.021935 restraints weight = 69674.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.022118 restraints weight = 56458.527| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 36819 Z= 0.213 Angle : 0.779 12.572 54562 Z= 0.437 Chirality : 0.050 0.375 6894 Planarity : 0.007 0.088 3326 Dihedral : 23.995 178.074 17104 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.21 % Allowed : 17.61 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.25 (0.19), residues: 1660 helix: -0.70 (0.18), residues: 687 sheet: -0.77 (0.30), residues: 293 loop : -0.77 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 77 TYR 0.031 0.003 TYR D 75 PHE 0.034 0.003 PHE F 80 TRP 0.015 0.003 TRP X 113 HIS 0.011 0.002 HIS L 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.21 (36819) covalent geometry : angle 0.77926 / 0.44 (54562) hydrogen bonds : bond 0.09240 / 9.87 ( 1506) hydrogen bonds : angle 4.95641 / 6.58 ( 3181) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 390 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7536 (t80) cc_final: 0.7130 (t80) REVERT: D 51 TYR cc_start: 0.9436 (t80) cc_final: 0.8966 (t80) REVERT: D 71 GLN cc_start: 0.9095 (mt0) cc_final: 0.8734 (mt0) REVERT: D 74 ASN cc_start: 0.9236 (m-40) cc_final: 0.8683 (m-40) REVERT: D 75 TYR cc_start: 0.9372 (m-80) cc_final: 0.9028 (m-80) REVERT: D 77 LYS cc_start: 0.9614 (mtmt) cc_final: 0.9332 (mtmm) REVERT: D 132 ILE cc_start: 0.9387 (mm) cc_final: 0.9071 (mm) REVERT: D 182 PHE cc_start: 0.9361 (t80) cc_final: 0.9090 (t80) REVERT: D 196 ASN cc_start: 0.9025 (m-40) cc_final: 0.8651 (m110) REVERT: E 12 GLN cc_start: 0.8956 (tp40) cc_final: 0.8158 (tm-30) REVERT: E 13 GLU cc_start: 0.9471 (pm20) cc_final: 0.9037 (pp20) REVERT: E 30 ILE cc_start: 0.8089 (mm) cc_final: 0.7776 (mm) REVERT: E 37 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9080 (t) REVERT: E 54 ARG cc_start: 0.9104 (mmm160) cc_final: 0.8803 (mpt180) REVERT: E 62 LYS cc_start: 0.8323 (mmmm) cc_final: 0.8071 (mtmm) REVERT: E 65 GLU cc_start: 0.9429 (tp30) cc_final: 0.9037 (tp30) REVERT: E 66 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8323 (mmmt) REVERT: E 95 PHE cc_start: 0.9057 (t80) cc_final: 0.8773 (t80) REVERT: F 5 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7897 (mm-30) REVERT: F 65 GLU cc_start: 0.8864 (pt0) cc_final: 0.8504 (tt0) REVERT: F 88 MET cc_start: 0.9024 (ttm) cc_final: 0.8393 (ttm) REVERT: F 90 MET cc_start: 0.8370 (mmm) cc_final: 0.7870 (mmt) REVERT: F 91 ARG cc_start: 0.8850 (ttt180) cc_final: 0.8617 (ttt180) REVERT: F 92 THR cc_start: 0.9015 (p) cc_final: 0.8736 (p) REVERT: H 38 ASN cc_start: 0.9461 (t0) cc_final: 0.8920 (t0) REVERT: H 43 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8803 (tp30) REVERT: H 80 ARG cc_start: 0.8599 (mtp-110) cc_final: 0.8396 (mtp-110) REVERT: H 85 ILE cc_start: 0.9448 (mm) cc_final: 0.9016 (mp) REVERT: H 86 TYR cc_start: 0.8518 (m-80) cc_final: 0.7352 (m-10) REVERT: H 124 GLU cc_start: 0.9243 (tt0) cc_final: 0.8403 (tt0) REVERT: H 127 CYS cc_start: 0.9641 (p) cc_final: 0.9304 (p) REVERT: H 128 TYR cc_start: 0.9218 (m-10) cc_final: 0.8792 (m-80) REVERT: K 125 LYS cc_start: 0.9542 (pttt) cc_final: 0.9162 (ptpp) REVERT: L 5 ASN cc_start: 0.9475 (t0) cc_final: 0.9021 (t0) REVERT: L 73 ASN cc_start: 0.8658 (p0) cc_final: 0.8450 (p0) REVERT: L 103 ASP cc_start: 0.9323 (t0) cc_final: 0.8901 (t0) REVERT: L 117 TYR cc_start: 0.8655 (m-80) cc_final: 0.8394 (m-10) REVERT: O 68 ASP cc_start: 0.9406 (m-30) cc_final: 0.9146 (m-30) REVERT: O 87 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8896 (mm) REVERT: P 26 ASN cc_start: 0.9000 (m110) cc_final: 0.8691 (m110) REVERT: Q 33 ILE cc_start: 0.9776 (mp) cc_final: 0.9568 (tp) REVERT: Q 38 ILE cc_start: 0.9736 (pt) cc_final: 0.9526 (mm) REVERT: T 13 GLN cc_start: 0.9576 (pt0) cc_final: 0.9208 (pp30) REVERT: U 19 PHE cc_start: 0.8129 (t80) cc_final: 0.7788 (t80) REVERT: U 23 CYS cc_start: 0.8632 (p) cc_final: 0.8322 (p) REVERT: U 35 ARG cc_start: 0.9170 (ttm170) cc_final: 0.8774 (mtt180) REVERT: U 36 GLU cc_start: 0.9695 (tp30) cc_final: 0.9263 (tp30) REVERT: U 40 LYS cc_start: 0.9613 (mtpt) cc_final: 0.9354 (ttpt) REVERT: X 62 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8445 (pp) REVERT: X 101 LEU cc_start: 0.9351 (mp) cc_final: 0.9015 (tp) REVERT: Y 24 PHE cc_start: 0.8399 (m-80) cc_final: 0.7827 (m-80) REVERT: Y 41 MET cc_start: 0.8643 (mmm) cc_final: 0.8207 (mmm) REVERT: Y 116 TYR cc_start: 0.8056 (m-80) cc_final: 0.7306 (m-80) REVERT: Y 136 MET cc_start: 0.8664 (mpt) cc_final: 0.8357 (mpp) REVERT: Y 159 ARG cc_start: 0.9070 (tmt170) cc_final: 0.8700 (tmm-80) REVERT: Y 163 MET cc_start: 0.9658 (mmm) cc_final: 0.8888 (mmm) REVERT: Y 194 LEU cc_start: 0.9440 (pt) cc_final: 0.9151 (pt) REVERT: Y 200 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8194 (mmp) REVERT: Y 202 HIS cc_start: 0.9313 (m90) cc_final: 0.9052 (m90) REVERT: Y 241 MET cc_start: 0.9431 (mmm) cc_final: 0.8781 (mmt) REVERT: Y 247 MET cc_start: 0.8956 (mtm) cc_final: 0.8342 (mtp) outliers start: 45 outliers final: 18 residues processed: 415 average time/residue: 0.2387 time to fit residues: 150.6626 Evaluate side-chains 348 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 326 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 72 TYR Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 200 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [238, 70, 94, 140, 222, 82, 180, 220, 206, 168, 171] chunk 238 optimal weight: 5.9990 chunk 70 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 140 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 82 optimal weight: 30.0000 chunk 180 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 206 optimal weight: 0.8980 chunk 168 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 89 ASN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.025525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.020317 restraints weight = 429851.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.021148 restraints weight = 167634.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.021672 restraints weight = 96063.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.021991 restraints weight = 67302.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.022181 restraints weight = 53740.509| |-----------------------------------------------------------------------------| r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36819 Z= 0.164 Angle : 0.639 10.334 54562 Z= 0.368 Chirality : 0.041 0.330 6894 Planarity : 0.006 0.077 3326 Dihedral : 23.866 179.954 17103 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.06 % Allowed : 19.67 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.20), residues: 1660 helix: -0.41 (0.18), residues: 691 sheet: -0.86 (0.29), residues: 308 loop : -0.71 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG T 29 TYR 0.024 0.002 TYR R 70 PHE 0.026 0.002 PHE F 80 TRP 0.017 0.003 TRP X 113 HIS 0.010 0.001 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (36819) covalent geometry : angle 0.63869 / 0.37 (54562) hydrogen bonds : bond 0.07545 / 8.06 ( 1506) hydrogen bonds : angle 4.64232 / 6.07 ( 3181) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 364 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7288 (t80) cc_final: 0.6914 (t80) REVERT: D 51 TYR cc_start: 0.9394 (t80) cc_final: 0.9030 (t80) REVERT: D 71 GLN cc_start: 0.9004 (mt0) cc_final: 0.8666 (mt0) REVERT: D 75 TYR cc_start: 0.9417 (m-80) cc_final: 0.9022 (m-80) REVERT: D 76 TYR cc_start: 0.9609 (t80) cc_final: 0.9407 (t80) REVERT: D 77 LYS cc_start: 0.9599 (mtmt) cc_final: 0.9328 (mtmt) REVERT: D 78 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.9124 (tp30) REVERT: D 132 ILE cc_start: 0.9408 (mm) cc_final: 0.9134 (mm) REVERT: D 182 PHE cc_start: 0.9339 (t80) cc_final: 0.9064 (t80) REVERT: D 196 ASN cc_start: 0.9008 (m-40) cc_final: 0.8619 (m110) REVERT: E 12 GLN cc_start: 0.8924 (tp40) cc_final: 0.8182 (tm-30) REVERT: E 16 ILE cc_start: 0.9603 (tp) cc_final: 0.9334 (mp) REVERT: E 30 ILE cc_start: 0.7998 (mm) cc_final: 0.7633 (mm) REVERT: E 37 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9025 (t) REVERT: E 54 ARG cc_start: 0.9140 (mmm160) cc_final: 0.8926 (mpt180) REVERT: E 62 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7796 (mtmm) REVERT: E 64 MET cc_start: 0.9581 (mmt) cc_final: 0.9063 (mmt) REVERT: E 65 GLU cc_start: 0.9501 (tp30) cc_final: 0.8969 (tp30) REVERT: E 66 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8492 (mmmt) REVERT: E 95 PHE cc_start: 0.9161 (t80) cc_final: 0.8826 (t80) REVERT: E 126 LYS cc_start: 0.9160 (tptt) cc_final: 0.8685 (tppt) REVERT: E 144 LEU cc_start: 0.9575 (mm) cc_final: 0.9362 (mm) REVERT: F 24 ARG cc_start: 0.9064 (ptp90) cc_final: 0.8823 (ptp-110) REVERT: F 88 MET cc_start: 0.8787 (ttm) cc_final: 0.8449 (ttm) REVERT: F 90 MET cc_start: 0.8247 (mmm) cc_final: 0.7851 (mmm) REVERT: F 91 ARG cc_start: 0.8861 (ttt180) cc_final: 0.8544 (ttt180) REVERT: H 38 ASN cc_start: 0.9458 (t0) cc_final: 0.8999 (t0) REVERT: H 42 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9081 (mm-30) REVERT: H 43 GLU cc_start: 0.9267 (mm-30) cc_final: 0.9004 (tp30) REVERT: H 80 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.8259 (mtp-110) REVERT: H 85 ILE cc_start: 0.9438 (mm) cc_final: 0.9037 (mm) REVERT: H 86 TYR cc_start: 0.8417 (m-80) cc_final: 0.7469 (m-10) REVERT: H 124 GLU cc_start: 0.9364 (tt0) cc_final: 0.8569 (tt0) REVERT: H 127 CYS cc_start: 0.9743 (p) cc_final: 0.9437 (p) REVERT: K 107 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8813 (mp) REVERT: L 5 ASN cc_start: 0.9503 (t0) cc_final: 0.9162 (t0) REVERT: L 7 LEU cc_start: 0.9902 (mm) cc_final: 0.9691 (mp) REVERT: L 73 ASN cc_start: 0.8747 (p0) cc_final: 0.8510 (p0) REVERT: L 90 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8554 (mm) REVERT: L 103 ASP cc_start: 0.9356 (t0) cc_final: 0.8990 (t0) REVERT: O 68 ASP cc_start: 0.9389 (m-30) cc_final: 0.9132 (m-30) REVERT: P 1 MET cc_start: 0.8615 (pmm) cc_final: 0.8384 (pmm) REVERT: P 26 ASN cc_start: 0.8924 (m110) cc_final: 0.8624 (m110) REVERT: P 52 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8919 (pp) REVERT: P 53 ASP cc_start: 0.9379 (t0) cc_final: 0.9011 (t0) REVERT: Q 39 LYS cc_start: 0.9709 (mmmt) cc_final: 0.9437 (mmmt) REVERT: Q 80 GLU cc_start: 0.8918 (tp30) cc_final: 0.8434 (tm-30) REVERT: R 64 TYR cc_start: 0.9247 (t80) cc_final: 0.8927 (t80) REVERT: T 13 GLN cc_start: 0.9579 (pt0) cc_final: 0.9177 (pp30) REVERT: T 29 ARG cc_start: 0.9366 (ptp90) cc_final: 0.9128 (ptp90) REVERT: U 19 PHE cc_start: 0.8294 (t80) cc_final: 0.7999 (t80) REVERT: U 23 CYS cc_start: 0.8662 (p) cc_final: 0.8375 (p) REVERT: U 35 ARG cc_start: 0.9017 (ttm170) cc_final: 0.8429 (mmt90) REVERT: U 36 GLU cc_start: 0.9732 (tp30) cc_final: 0.9196 (tp30) REVERT: U 40 LYS cc_start: 0.9618 (mtpt) cc_final: 0.9193 (mtpp) REVERT: X 35 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9021 (m) REVERT: X 101 LEU cc_start: 0.9349 (mp) cc_final: 0.8954 (tp) REVERT: Y 113 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8806 (t0) REVERT: Y 136 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8166 (mpp) REVERT: Y 155 LYS cc_start: 0.9113 (tppt) cc_final: 0.8806 (tppt) REVERT: Y 159 ARG cc_start: 0.9103 (tmt170) cc_final: 0.8625 (tmm-80) REVERT: Y 163 MET cc_start: 0.9630 (mmm) cc_final: 0.8732 (mmm) REVERT: Y 194 LEU cc_start: 0.9452 (pt) cc_final: 0.9227 (pt) REVERT: Y 241 MET cc_start: 0.9427 (mmm) cc_final: 0.8761 (mmt) REVERT: Y 247 MET cc_start: 0.9119 (mtm) cc_final: 0.8810 (mpp) outliers start: 43 outliers final: 18 residues processed: 388 average time/residue: 0.2340 time to fit residues: 139.3540 Evaluate side-chains 349 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 323 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 113 ASN Chi-restraints excluded: chain Y residue 136 MET Chi-restraints excluded: chain Y residue 143 GLU Chi-restraints excluded: chain Y residue 200 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [26, 157, 147, 238, 146, 36, 192, 131, 33, 158, 106] chunk 26 optimal weight: 30.0000 chunk 157 optimal weight: 20.0000 chunk 147 optimal weight: 0.3980 chunk 238 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 36 optimal weight: 30.0000 chunk 192 optimal weight: 0.7980 chunk 131 optimal weight: 0.0470 chunk 33 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 overall best weight: 2.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN F 55 HIS H 76 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN X 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.025690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.020494 restraints weight = 424519.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.021324 restraints weight = 167937.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.021840 restraints weight = 96606.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.022163 restraints weight = 67756.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.022359 restraints weight = 54070.907| |-----------------------------------------------------------------------------| r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36819 Z= 0.143 Angle : 0.607 13.584 54562 Z= 0.344 Chirality : 0.038 0.326 6894 Planarity : 0.005 0.055 3326 Dihedral : 23.789 178.886 17103 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.92 % Allowed : 21.53 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.20), residues: 1660 helix: -0.19 (0.19), residues: 693 sheet: -0.73 (0.29), residues: 303 loop : -0.79 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG O 89 TYR 0.021 0.002 TYR H 128 PHE 0.023 0.002 PHE F 80 TRP 0.016 0.002 TRP F 42 HIS 0.009 0.001 HIS L 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (36819) covalent geometry : angle 0.60656 / 0.34 (54562) hydrogen bonds : bond 0.07084 / 7.60 ( 1506) hydrogen bonds : angle 4.52055 / 5.95 ( 3181) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 352 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7367 (t80) cc_final: 0.7014 (t80) REVERT: D 51 TYR cc_start: 0.9361 (t80) cc_final: 0.8884 (t80) REVERT: D 71 GLN cc_start: 0.8823 (mt0) cc_final: 0.8491 (mt0) REVERT: D 75 TYR cc_start: 0.9422 (m-80) cc_final: 0.9078 (m-80) REVERT: D 77 LYS cc_start: 0.9608 (mtmt) cc_final: 0.9347 (mtmm) REVERT: D 132 ILE cc_start: 0.9424 (mm) cc_final: 0.9190 (mm) REVERT: D 182 PHE cc_start: 0.9311 (t80) cc_final: 0.9071 (t80) REVERT: D 196 ASN cc_start: 0.8991 (m-40) cc_final: 0.8644 (m110) REVERT: E 12 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8342 (tm-30) REVERT: E 14 LYS cc_start: 0.9586 (tppp) cc_final: 0.9351 (ttmm) REVERT: E 16 ILE cc_start: 0.9553 (tp) cc_final: 0.9264 (mp) REVERT: E 30 ILE cc_start: 0.8301 (mm) cc_final: 0.7949 (mm) REVERT: E 37 THR cc_start: 0.9475 (m) cc_final: 0.9221 (t) REVERT: E 54 ARG cc_start: 0.9019 (mmm160) cc_final: 0.8774 (mpt180) REVERT: E 60 ILE cc_start: 0.9540 (OUTLIER) cc_final: 0.8917 (tt) REVERT: E 62 LYS cc_start: 0.7973 (mmmm) cc_final: 0.7766 (mtmm) REVERT: E 65 GLU cc_start: 0.9455 (tp30) cc_final: 0.8969 (tp30) REVERT: E 66 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8523 (mmmt) REVERT: E 68 ARG cc_start: 0.8670 (ptp-110) cc_final: 0.8108 (ptp-170) REVERT: E 95 PHE cc_start: 0.9206 (t80) cc_final: 0.8820 (t80) REVERT: E 126 LYS cc_start: 0.9196 (tptt) cc_final: 0.8740 (tppt) REVERT: E 144 LEU cc_start: 0.9598 (mm) cc_final: 0.9333 (mm) REVERT: F 90 MET cc_start: 0.8228 (mmm) cc_final: 0.7621 (mmm) REVERT: H 38 ASN cc_start: 0.9453 (t0) cc_final: 0.8922 (t0) REVERT: H 42 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8992 (mm-30) REVERT: H 43 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8864 (tp30) REVERT: H 80 ARG cc_start: 0.8894 (mtp-110) cc_final: 0.8556 (mtp-110) REVERT: H 85 ILE cc_start: 0.9491 (mm) cc_final: 0.9124 (mm) REVERT: H 86 TYR cc_start: 0.8471 (m-80) cc_final: 0.7336 (m-10) REVERT: H 101 ILE cc_start: 0.9360 (mm) cc_final: 0.9089 (mm) REVERT: H 124 GLU cc_start: 0.9338 (tt0) cc_final: 0.8427 (tt0) REVERT: H 127 CYS cc_start: 0.9624 (p) cc_final: 0.9140 (m) REVERT: K 107 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8682 (mp) REVERT: L 5 ASN cc_start: 0.9533 (t0) cc_final: 0.9137 (t0) REVERT: L 73 ASN cc_start: 0.8871 (p0) cc_final: 0.8580 (p0) REVERT: L 90 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8679 (mm) REVERT: L 103 ASP cc_start: 0.9324 (t0) cc_final: 0.9075 (t0) REVERT: O 65 LYS cc_start: 0.9640 (mtpt) cc_final: 0.9376 (ptpp) REVERT: O 68 ASP cc_start: 0.9373 (m-30) cc_final: 0.9121 (m-30) REVERT: P 1 MET cc_start: 0.8670 (pmm) cc_final: 0.8445 (pmm) REVERT: P 26 ASN cc_start: 0.8984 (m110) cc_final: 0.8687 (m110) REVERT: P 52 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8716 (pp) REVERT: P 53 ASP cc_start: 0.9347 (t0) cc_final: 0.8878 (t0) REVERT: Q 39 LYS cc_start: 0.9724 (mmmt) cc_final: 0.9468 (mmmt) REVERT: Q 44 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8352 (tt) REVERT: Q 62 ARG cc_start: 0.9380 (ttp80) cc_final: 0.9093 (ttp80) REVERT: T 13 GLN cc_start: 0.9526 (pt0) cc_final: 0.9145 (pp30) REVERT: U 19 PHE cc_start: 0.8408 (t80) cc_final: 0.8092 (t80) REVERT: U 23 CYS cc_start: 0.8678 (p) cc_final: 0.8382 (p) REVERT: U 35 ARG cc_start: 0.8960 (ttm170) cc_final: 0.8410 (mmt90) REVERT: U 36 GLU cc_start: 0.9727 (tp30) cc_final: 0.9186 (tp30) REVERT: U 40 LYS cc_start: 0.9609 (mtpt) cc_final: 0.9151 (mtpp) REVERT: U 42 THR cc_start: 0.9195 (t) cc_final: 0.8937 (m) REVERT: X 35 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9031 (m) REVERT: X 105 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.5936 (pmm) REVERT: Y 116 TYR cc_start: 0.7820 (m-80) cc_final: 0.6929 (m-80) REVERT: Y 136 MET cc_start: 0.8561 (mpt) cc_final: 0.8080 (mpp) REVERT: Y 163 MET cc_start: 0.9618 (mmm) cc_final: 0.9150 (mmm) REVERT: Y 194 LEU cc_start: 0.9398 (pt) cc_final: 0.9155 (pt) REVERT: Y 202 HIS cc_start: 0.9316 (m90) cc_final: 0.9080 (m90) REVERT: Y 241 MET cc_start: 0.9398 (mmm) cc_final: 0.8972 (mmm) REVERT: Y 247 MET cc_start: 0.9183 (mtm) cc_final: 0.8900 (mpp) outliers start: 41 outliers final: 21 residues processed: 377 average time/residue: 0.2298 time to fit residues: 134.1486 Evaluate side-chains 353 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 325 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [205, 258, 198, 166, 111, 118, 36, 45, 245, 77, 16] chunk 205 optimal weight: 10.0000 chunk 258 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 45 optimal weight: 30.0000 chunk 245 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 16 optimal weight: 50.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN R 74 HIS X 109 ASN Y 197 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.024753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.019643 restraints weight = 439665.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.020430 restraints weight = 176665.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.020923 restraints weight = 102307.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.021232 restraints weight = 72297.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.021419 restraints weight = 58213.226| |-----------------------------------------------------------------------------| r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36819 Z= 0.232 Angle : 0.655 13.571 54562 Z= 0.364 Chirality : 0.041 0.333 6894 Planarity : 0.006 0.058 3326 Dihedral : 23.807 179.635 17103 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.56 % Allowed : 21.95 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.20), residues: 1660 helix: -0.38 (0.18), residues: 692 sheet: -0.88 (0.28), residues: 329 loop : -0.67 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 11 TYR 0.033 0.003 TYR D 76 PHE 0.043 0.002 PHE F 80 TRP 0.007 0.002 TRP D 170 HIS 0.009 0.002 HIS L 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.23 (36819) covalent geometry : angle 0.65483 / 0.36 (54562) hydrogen bonds : bond 0.08856 / 9.52 ( 1506) hydrogen bonds : angle 4.61895 / 6.06 ( 3181) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 333 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7580 (t80) cc_final: 0.7203 (t80) REVERT: D 51 TYR cc_start: 0.9365 (t80) cc_final: 0.8944 (t80) REVERT: D 71 GLN cc_start: 0.8740 (mt0) cc_final: 0.8470 (mt0) REVERT: D 182 PHE cc_start: 0.9245 (t80) cc_final: 0.9005 (t80) REVERT: D 196 ASN cc_start: 0.9011 (m-40) cc_final: 0.8570 (m110) REVERT: E 12 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8400 (tm-30) REVERT: E 16 ILE cc_start: 0.9549 (tp) cc_final: 0.9314 (mp) REVERT: E 30 ILE cc_start: 0.8349 (mm) cc_final: 0.7996 (mm) REVERT: E 54 ARG cc_start: 0.8982 (mmm160) cc_final: 0.8692 (mpt180) REVERT: E 60 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9180 (pt) REVERT: E 62 LYS cc_start: 0.7941 (mmmm) cc_final: 0.7659 (mtmm) REVERT: E 65 GLU cc_start: 0.9473 (tp30) cc_final: 0.8895 (tp30) REVERT: E 66 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8485 (mmmt) REVERT: E 95 PHE cc_start: 0.9226 (t80) cc_final: 0.8879 (t80) REVERT: E 126 LYS cc_start: 0.9199 (tptt) cc_final: 0.8695 (tppt) REVERT: F 9 MET cc_start: 0.9119 (pmm) cc_final: 0.8676 (pmm) REVERT: F 88 MET cc_start: 0.8597 (ttt) cc_final: 0.8171 (tmm) REVERT: H 38 ASN cc_start: 0.9434 (t0) cc_final: 0.8924 (t0) REVERT: H 80 ARG cc_start: 0.8951 (mtp-110) cc_final: 0.8605 (mtp-110) REVERT: H 85 ILE cc_start: 0.9443 (mm) cc_final: 0.9097 (mm) REVERT: H 86 TYR cc_start: 0.8597 (m-80) cc_final: 0.7367 (m-80) REVERT: H 96 MET cc_start: 0.9271 (mtm) cc_final: 0.8720 (ptp) REVERT: H 124 GLU cc_start: 0.9298 (tt0) cc_final: 0.8430 (tt0) REVERT: K 125 LYS cc_start: 0.9573 (pttt) cc_final: 0.9365 (ptpt) REVERT: L 5 ASN cc_start: 0.9570 (t0) cc_final: 0.9183 (t0) REVERT: L 103 ASP cc_start: 0.9350 (t0) cc_final: 0.9137 (t0) REVERT: O 26 GLU cc_start: 0.9442 (mp0) cc_final: 0.9169 (pm20) REVERT: O 58 ARG cc_start: 0.9392 (ttt-90) cc_final: 0.9147 (ptm-80) REVERT: O 65 LYS cc_start: 0.9702 (mtpt) cc_final: 0.9377 (ptpp) REVERT: O 68 ASP cc_start: 0.9330 (m-30) cc_final: 0.9110 (m-30) REVERT: P 1 MET cc_start: 0.8649 (pmm) cc_final: 0.8361 (pmm) REVERT: P 26 ASN cc_start: 0.9019 (m110) cc_final: 0.8719 (m110) REVERT: P 53 ASP cc_start: 0.9284 (t0) cc_final: 0.8840 (t0) REVERT: Q 39 LYS cc_start: 0.9725 (mmmt) cc_final: 0.9358 (mmmt) REVERT: Q 44 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8426 (tt) REVERT: Q 80 GLU cc_start: 0.9022 (tp30) cc_final: 0.8500 (tm-30) REVERT: T 13 GLN cc_start: 0.9548 (pt0) cc_final: 0.9113 (pp30) REVERT: T 29 ARG cc_start: 0.9406 (OUTLIER) cc_final: 0.9180 (ptp90) REVERT: U 23 CYS cc_start: 0.8750 (p) cc_final: 0.8363 (p) REVERT: U 35 ARG cc_start: 0.9011 (ttm170) cc_final: 0.8525 (mmt90) REVERT: U 36 GLU cc_start: 0.9726 (tp30) cc_final: 0.9200 (tp30) REVERT: X 105 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5990 (pmm) REVERT: Y 116 TYR cc_start: 0.7779 (m-80) cc_final: 0.6793 (m-80) REVERT: Y 136 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8130 (mpp) REVERT: Y 163 MET cc_start: 0.9603 (mmm) cc_final: 0.9150 (mmm) REVERT: Y 202 HIS cc_start: 0.9313 (m90) cc_final: 0.9067 (m90) REVERT: Y 241 MET cc_start: 0.9429 (mmm) cc_final: 0.9024 (mmm) REVERT: Y 247 MET cc_start: 0.9280 (mtm) cc_final: 0.9064 (mtp) outliers start: 64 outliers final: 35 residues processed: 374 average time/residue: 0.2301 time to fit residues: 133.0438 Evaluate side-chains 348 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 136 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [176, 54, 220, 165, 63, 7, 109, 258, 112, 255, 23] chunk 176 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 220 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 7 optimal weight: 40.0000 chunk 109 optimal weight: 5.9990 chunk 258 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 63 ASN H 76 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.025376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.020176 restraints weight = 428250.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.021006 restraints weight = 167764.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.021523 restraints weight = 96364.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.021839 restraints weight = 67659.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.022034 restraints weight = 53969.490| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 36819 Z= 0.146 Angle : 0.607 13.457 54562 Z= 0.337 Chirality : 0.038 0.331 6894 Planarity : 0.005 0.065 3326 Dihedral : 23.857 179.400 17103 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.92 % Allowed : 24.45 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1660 helix: -0.21 (0.19), residues: 694 sheet: -0.86 (0.28), residues: 322 loop : -0.65 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 11 TYR 0.028 0.002 TYR D 75 PHE 0.044 0.002 PHE F 80 TRP 0.008 0.002 TRP F 42 HIS 0.011 0.001 HIS L 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (36819) covalent geometry : angle 0.60677 / 0.34 (54562) hydrogen bonds : bond 0.07084 / 7.60 ( 1506) hydrogen bonds : angle 4.48836 / 5.89 ( 3181) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 349 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7361 (t80) cc_final: 0.7044 (t80) REVERT: D 51 TYR cc_start: 0.9302 (t80) cc_final: 0.8944 (t80) REVERT: D 74 ASN cc_start: 0.9230 (m-40) cc_final: 0.8788 (m-40) REVERT: D 182 PHE cc_start: 0.9218 (t80) cc_final: 0.8943 (t80) REVERT: D 196 ASN cc_start: 0.9041 (m-40) cc_final: 0.8589 (m110) REVERT: E 12 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8369 (tm-30) REVERT: E 16 ILE cc_start: 0.9534 (tp) cc_final: 0.9302 (mp) REVERT: E 30 ILE cc_start: 0.8327 (mm) cc_final: 0.7979 (mm) REVERT: E 54 ARG cc_start: 0.8913 (mmm160) cc_final: 0.8638 (mpt180) REVERT: E 60 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9169 (pt) REVERT: E 62 LYS cc_start: 0.7634 (mmmm) cc_final: 0.7358 (mtmm) REVERT: E 65 GLU cc_start: 0.9486 (tp30) cc_final: 0.8845 (tp30) REVERT: E 66 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8424 (mmmt) REVERT: E 95 PHE cc_start: 0.9227 (t80) cc_final: 0.8769 (t80) REVERT: E 126 LYS cc_start: 0.9181 (tptt) cc_final: 0.8725 (tppt) REVERT: H 38 ASN cc_start: 0.9433 (t0) cc_final: 0.9075 (t0) REVERT: H 43 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8808 (tp30) REVERT: H 80 ARG cc_start: 0.9034 (mtp-110) cc_final: 0.8653 (mtp-110) REVERT: H 85 ILE cc_start: 0.9446 (mm) cc_final: 0.9103 (mm) REVERT: H 86 TYR cc_start: 0.8526 (m-80) cc_final: 0.7652 (m-10) REVERT: H 96 MET cc_start: 0.9242 (mtm) cc_final: 0.8677 (ptp) REVERT: H 101 ILE cc_start: 0.9177 (mm) cc_final: 0.8953 (mm) REVERT: H 124 GLU cc_start: 0.9356 (tt0) cc_final: 0.8531 (tt0) REVERT: K 42 LEU cc_start: 0.8711 (mm) cc_final: 0.8235 (mm) REVERT: K 77 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8382 (t80) REVERT: L 5 ASN cc_start: 0.9563 (t0) cc_final: 0.9143 (t0) REVERT: L 90 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8721 (mm) REVERT: O 26 GLU cc_start: 0.9436 (mp0) cc_final: 0.9126 (pm20) REVERT: O 58 ARG cc_start: 0.9320 (ttt-90) cc_final: 0.9101 (ptm-80) REVERT: O 59 MET cc_start: 0.9105 (mmp) cc_final: 0.7499 (mmp) REVERT: O 65 LYS cc_start: 0.9708 (mtpt) cc_final: 0.9389 (ptpp) REVERT: O 68 ASP cc_start: 0.9382 (m-30) cc_final: 0.9135 (m-30) REVERT: P 1 MET cc_start: 0.8658 (pmm) cc_final: 0.8419 (pmm) REVERT: P 26 ASN cc_start: 0.9002 (m110) cc_final: 0.8691 (m110) REVERT: P 53 ASP cc_start: 0.9330 (t0) cc_final: 0.8913 (t0) REVERT: Q 39 LYS cc_start: 0.9689 (mmmt) cc_final: 0.9450 (mmmt) REVERT: Q 62 ARG cc_start: 0.9514 (ttp80) cc_final: 0.9158 (ttp80) REVERT: R 61 ARG cc_start: 0.9621 (OUTLIER) cc_final: 0.9298 (mmm-85) REVERT: R 64 TYR cc_start: 0.9185 (t80) cc_final: 0.8828 (t80) REVERT: T 13 GLN cc_start: 0.9509 (pt0) cc_final: 0.9143 (pp30) REVERT: T 29 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.9188 (ptp90) REVERT: U 23 CYS cc_start: 0.8705 (p) cc_final: 0.8324 (p) REVERT: U 35 ARG cc_start: 0.8954 (ttm170) cc_final: 0.8476 (mmt90) REVERT: U 36 GLU cc_start: 0.9749 (tp30) cc_final: 0.9275 (tp30) REVERT: U 40 LYS cc_start: 0.9482 (mtpt) cc_final: 0.9096 (mtpt) REVERT: X 108 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8061 (tp40) REVERT: Y 116 TYR cc_start: 0.7635 (m-80) cc_final: 0.6719 (m-80) REVERT: Y 136 MET cc_start: 0.8513 (mpt) cc_final: 0.8163 (mpp) REVERT: Y 163 MET cc_start: 0.9590 (mmm) cc_final: 0.9146 (mmm) REVERT: Y 241 MET cc_start: 0.9393 (mmm) cc_final: 0.8982 (mmm) REVERT: Y 247 MET cc_start: 0.9287 (mtm) cc_final: 0.8837 (mtp) outliers start: 55 outliers final: 33 residues processed: 385 average time/residue: 0.2321 time to fit residues: 138.2991 Evaluate side-chains 357 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 318 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 108 GLN Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 226 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [1, 139, 172, 3, 41, 66, 206, 167, 254, 51, 113] chunk 1 optimal weight: 30.0000 chunk 139 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 41 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 206 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 51 optimal weight: 40.0000 chunk 113 optimal weight: 0.0470 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 GLN F 3 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN Q 9 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.025560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.020343 restraints weight = 430140.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.021162 restraints weight = 168433.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.021682 restraints weight = 96191.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.021997 restraints weight = 67549.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.022173 restraints weight = 53986.440| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36819 Z= 0.142 Angle : 0.611 16.356 54562 Z= 0.339 Chirality : 0.037 0.350 6894 Planarity : 0.005 0.069 3326 Dihedral : 23.802 179.964 17103 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.85 % Allowed : 25.87 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.20), residues: 1660 helix: -0.21 (0.19), residues: 693 sheet: -0.89 (0.28), residues: 315 loop : -0.62 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 11 TYR 0.020 0.002 TYR K 77 PHE 0.044 0.002 PHE F 80 TRP 0.008 0.002 TRP Q 73 HIS 0.010 0.001 HIS L 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (36819) covalent geometry : angle 0.61083 / 0.34 (54562) hydrogen bonds : bond 0.06884 / 7.38 ( 1506) hydrogen bonds : angle 4.48891 / 5.79 ( 3181) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 331 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7382 (t80) cc_final: 0.7073 (t80) REVERT: D 51 TYR cc_start: 0.9157 (t80) cc_final: 0.8674 (t80) REVERT: D 75 TYR cc_start: 0.9301 (m-80) cc_final: 0.8993 (m-80) REVERT: D 182 PHE cc_start: 0.9206 (t80) cc_final: 0.8921 (t80) REVERT: D 196 ASN cc_start: 0.9060 (m-40) cc_final: 0.8592 (m110) REVERT: E 12 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8362 (tm-30) REVERT: E 16 ILE cc_start: 0.9526 (tp) cc_final: 0.9288 (mp) REVERT: E 30 ILE cc_start: 0.8384 (mm) cc_final: 0.8043 (mm) REVERT: E 54 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8625 (mpt180) REVERT: E 62 LYS cc_start: 0.7579 (mmmm) cc_final: 0.7321 (mtmm) REVERT: E 65 GLU cc_start: 0.9415 (tp30) cc_final: 0.8850 (tp30) REVERT: E 66 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8429 (mmmt) REVERT: E 95 PHE cc_start: 0.9269 (t80) cc_final: 0.8805 (t80) REVERT: E 126 LYS cc_start: 0.9129 (tptt) cc_final: 0.8707 (tppt) REVERT: E 147 MET cc_start: 0.8612 (tpt) cc_final: 0.8294 (tpt) REVERT: F 5 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8274 (mm-30) REVERT: F 33 GLU cc_start: 0.9461 (mp0) cc_final: 0.9260 (pm20) REVERT: F 91 ARG cc_start: 0.8896 (tpp80) cc_final: 0.8094 (ttt180) REVERT: H 38 ASN cc_start: 0.9412 (t0) cc_final: 0.9115 (t0) REVERT: H 43 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8735 (tp30) REVERT: H 80 ARG cc_start: 0.9040 (mtp-110) cc_final: 0.8530 (mtp-110) REVERT: H 85 ILE cc_start: 0.9432 (mm) cc_final: 0.9076 (mm) REVERT: H 86 TYR cc_start: 0.8534 (m-80) cc_final: 0.7649 (m-10) REVERT: H 96 MET cc_start: 0.9266 (mtm) cc_final: 0.8692 (ptp) REVERT: H 124 GLU cc_start: 0.9367 (tt0) cc_final: 0.8563 (tt0) REVERT: K 42 LEU cc_start: 0.8722 (mm) cc_final: 0.8261 (mm) REVERT: K 125 LYS cc_start: 0.9306 (ptpt) cc_final: 0.9105 (ptpt) REVERT: L 5 ASN cc_start: 0.9562 (t0) cc_final: 0.9148 (t0) REVERT: L 90 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8725 (mm) REVERT: O 26 GLU cc_start: 0.9433 (mp0) cc_final: 0.9120 (pm20) REVERT: O 58 ARG cc_start: 0.9298 (ttt-90) cc_final: 0.9082 (ptm-80) REVERT: O 59 MET cc_start: 0.9046 (mmp) cc_final: 0.7371 (mmp) REVERT: O 65 LYS cc_start: 0.9702 (mtpt) cc_final: 0.9381 (ptpp) REVERT: O 68 ASP cc_start: 0.9405 (m-30) cc_final: 0.9194 (m-30) REVERT: P 1 MET cc_start: 0.8694 (pmm) cc_final: 0.8444 (pmm) REVERT: P 26 ASN cc_start: 0.9005 (m110) cc_final: 0.8679 (m110) REVERT: P 53 ASP cc_start: 0.9304 (t0) cc_final: 0.8944 (t0) REVERT: Q 49 GLU cc_start: 0.9032 (pm20) cc_final: 0.8762 (pm20) REVERT: Q 80 GLU cc_start: 0.8887 (tp30) cc_final: 0.8437 (tm-30) REVERT: T 13 GLN cc_start: 0.9486 (pt0) cc_final: 0.9130 (pp30) REVERT: U 23 CYS cc_start: 0.8730 (p) cc_final: 0.8328 (p) REVERT: U 35 ARG cc_start: 0.8947 (ttm170) cc_final: 0.8490 (mmt90) REVERT: U 36 GLU cc_start: 0.9760 (tp30) cc_final: 0.9487 (tp30) REVERT: U 37 PHE cc_start: 0.9273 (m-80) cc_final: 0.8434 (m-80) REVERT: U 40 LYS cc_start: 0.9515 (mtpt) cc_final: 0.9126 (mtpt) REVERT: X 108 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7662 (tp40) REVERT: X 145 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8423 (t0) REVERT: Y 104 MET cc_start: 0.7316 (tmm) cc_final: 0.7110 (ppp) REVERT: Y 116 TYR cc_start: 0.7661 (m-80) cc_final: 0.6717 (m-80) REVERT: Y 136 MET cc_start: 0.8474 (mpt) cc_final: 0.8199 (mpp) REVERT: Y 163 MET cc_start: 0.9609 (mmm) cc_final: 0.9170 (mmm) REVERT: Y 226 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8889 (tmm160) REVERT: Y 241 MET cc_start: 0.9397 (mmm) cc_final: 0.8985 (mmm) REVERT: Y 247 MET cc_start: 0.9287 (mtm) cc_final: 0.8893 (mtp) outliers start: 54 outliers final: 32 residues processed: 366 average time/residue: 0.2299 time to fit residues: 129.9671 Evaluate side-chains 351 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 108 GLN Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 202 HIS Chi-restraints excluded: chain Y residue 226 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [227, 188, 150, 198, 2, 239, 73, 173, 238, 1, 66] chunk 227 optimal weight: 20.0000 chunk 188 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 chunk 239 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 173 optimal weight: 10.0000 chunk 238 optimal weight: 0.7980 chunk 1 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 63 ASN H 76 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.025175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.020007 restraints weight = 436006.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.020807 restraints weight = 173826.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.021308 restraints weight = 99967.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.021623 restraints weight = 70514.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.021812 restraints weight = 56697.570| |-----------------------------------------------------------------------------| r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 36819 Z= 0.188 Angle : 0.639 15.645 54562 Z= 0.352 Chirality : 0.039 0.333 6894 Planarity : 0.005 0.065 3326 Dihedral : 23.800 179.617 17103 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.42 % Allowed : 26.73 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1660 helix: -0.28 (0.19), residues: 697 sheet: -1.10 (0.29), residues: 307 loop : -0.63 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 11 TYR 0.036 0.002 TYR K 77 PHE 0.049 0.002 PHE F 80 TRP 0.006 0.002 TRP Q 73 HIS 0.011 0.002 HIS F 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.19 (36819) covalent geometry : angle 0.63919 / 0.35 (54562) hydrogen bonds : bond 0.07610 / 8.17 ( 1506) hydrogen bonds : angle 4.52770 / 5.85 ( 3181) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 327 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7495 (t80) cc_final: 0.7190 (t80) REVERT: D 75 TYR cc_start: 0.9312 (m-80) cc_final: 0.8946 (m-80) REVERT: D 178 MET cc_start: 0.8619 (ptp) cc_final: 0.8254 (pmm) REVERT: D 182 PHE cc_start: 0.9183 (t80) cc_final: 0.8920 (t80) REVERT: D 196 ASN cc_start: 0.9086 (m-40) cc_final: 0.8627 (m110) REVERT: E 12 GLN cc_start: 0.8892 (tp-100) cc_final: 0.8373 (tm-30) REVERT: E 16 ILE cc_start: 0.9537 (tp) cc_final: 0.9301 (mp) REVERT: E 30 ILE cc_start: 0.8483 (mm) cc_final: 0.8134 (mm) REVERT: E 54 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8575 (mpt180) REVERT: E 62 LYS cc_start: 0.7336 (mmmm) cc_final: 0.7109 (mtmm) REVERT: E 65 GLU cc_start: 0.9429 (tp30) cc_final: 0.9064 (tp30) REVERT: E 66 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8551 (mmmt) REVERT: E 68 ARG cc_start: 0.9108 (ptp-110) cc_final: 0.8611 (ptp90) REVERT: E 71 MET cc_start: 0.8760 (mmm) cc_final: 0.7597 (mmm) REVERT: E 95 PHE cc_start: 0.9280 (t80) cc_final: 0.8809 (t80) REVERT: E 126 LYS cc_start: 0.9170 (tptt) cc_final: 0.8734 (tppt) REVERT: F 91 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8173 (ttt180) REVERT: H 38 ASN cc_start: 0.9453 (t0) cc_final: 0.9207 (t0) REVERT: H 43 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8462 (tp30) REVERT: H 80 ARG cc_start: 0.9076 (mtp-110) cc_final: 0.8575 (mtp-110) REVERT: H 85 ILE cc_start: 0.9467 (mm) cc_final: 0.9129 (mm) REVERT: H 86 TYR cc_start: 0.8603 (m-80) cc_final: 0.7577 (m-80) REVERT: H 124 GLU cc_start: 0.9332 (tt0) cc_final: 0.8525 (tt0) REVERT: H 128 TYR cc_start: 0.8964 (m-80) cc_final: 0.8479 (m-80) REVERT: K 42 LEU cc_start: 0.8704 (mm) cc_final: 0.8335 (mm) REVERT: K 125 LYS cc_start: 0.9372 (ptpt) cc_final: 0.9138 (ptpt) REVERT: L 5 ASN cc_start: 0.9577 (t0) cc_final: 0.9187 (t0) REVERT: O 65 LYS cc_start: 0.9708 (mtpt) cc_final: 0.9375 (ptpp) REVERT: P 1 MET cc_start: 0.8663 (pmm) cc_final: 0.8404 (pmm) REVERT: P 26 ASN cc_start: 0.9008 (m110) cc_final: 0.8689 (m110) REVERT: P 53 ASP cc_start: 0.9271 (t0) cc_final: 0.8905 (t0) REVERT: Q 34 TYR cc_start: 0.9382 (m-80) cc_final: 0.9122 (m-10) REVERT: Q 80 GLU cc_start: 0.8903 (tp30) cc_final: 0.8439 (tm-30) REVERT: T 13 GLN cc_start: 0.9477 (pt0) cc_final: 0.9070 (pp30) REVERT: U 23 CYS cc_start: 0.8748 (p) cc_final: 0.8327 (p) REVERT: U 35 ARG cc_start: 0.8977 (ttm170) cc_final: 0.8586 (mmt90) REVERT: U 36 GLU cc_start: 0.9751 (tp30) cc_final: 0.9486 (tp30) REVERT: U 37 PHE cc_start: 0.9281 (m-80) cc_final: 0.8501 (m-80) REVERT: U 40 LYS cc_start: 0.9563 (mtpt) cc_final: 0.9082 (mtpt) REVERT: X 108 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7765 (tp40) REVERT: X 145 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8395 (t0) REVERT: Y 104 MET cc_start: 0.7353 (tmm) cc_final: 0.7125 (ppp) REVERT: Y 116 TYR cc_start: 0.7701 (m-80) cc_final: 0.6739 (m-80) REVERT: Y 136 MET cc_start: 0.8479 (mpt) cc_final: 0.8223 (mpp) REVERT: Y 163 MET cc_start: 0.9615 (mmm) cc_final: 0.9190 (mmm) REVERT: Y 241 MET cc_start: 0.9398 (mmm) cc_final: 0.9029 (mmm) REVERT: Y 247 MET cc_start: 0.9285 (mtm) cc_final: 0.8889 (mtp) outliers start: 48 outliers final: 38 residues processed: 361 average time/residue: 0.2310 time to fit residues: 128.4336 Evaluate side-chains 351 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 311 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 108 GLN Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 226 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [60, 40, 157, 247, 256, 17, 146, 219, 39, 25, 169] chunk 60 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 157 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 256 optimal weight: 0.0170 chunk 17 optimal weight: 30.0000 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 39 optimal weight: 30.0000 chunk 25 optimal weight: 30.0000 chunk 169 optimal weight: 4.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 HIS F 63 ASN H 76 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.025212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.020054 restraints weight = 434995.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.020857 restraints weight = 172781.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.021356 restraints weight = 99489.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.021669 restraints weight = 70474.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.021829 restraints weight = 56598.658| |-----------------------------------------------------------------------------| r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36819 Z= 0.176 Angle : 0.642 15.116 54562 Z= 0.353 Chirality : 0.039 0.351 6894 Planarity : 0.005 0.063 3326 Dihedral : 23.829 179.285 17103 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.06 % Allowed : 27.44 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.20), residues: 1660 helix: -0.28 (0.19), residues: 699 sheet: -1.19 (0.28), residues: 306 loop : -0.71 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 69 TYR 0.031 0.002 TYR K 77 PHE 0.050 0.002 PHE F 80 TRP 0.006 0.001 TRP D 170 HIS 0.009 0.002 HIS L 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.18 (36819) covalent geometry : angle 0.64201 / 0.35 (54562) hydrogen bonds : bond 0.07372 / 7.90 ( 1506) hydrogen bonds : angle 4.52223 / 5.82 ( 3181) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 327 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7445 (t80) cc_final: 0.7119 (t80) REVERT: D 75 TYR cc_start: 0.9325 (m-80) cc_final: 0.8916 (m-80) REVERT: D 178 MET cc_start: 0.8681 (ptp) cc_final: 0.8455 (pmm) REVERT: D 182 PHE cc_start: 0.9178 (t80) cc_final: 0.8907 (t80) REVERT: D 196 ASN cc_start: 0.9086 (m-40) cc_final: 0.8632 (m110) REVERT: E 12 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8311 (tm-30) REVERT: E 16 ILE cc_start: 0.9538 (tp) cc_final: 0.9299 (mp) REVERT: E 30 ILE cc_start: 0.8534 (mm) cc_final: 0.8198 (mm) REVERT: E 54 ARG cc_start: 0.8906 (mmm160) cc_final: 0.8592 (mpt180) REVERT: E 62 LYS cc_start: 0.7322 (mmmm) cc_final: 0.7073 (mtmm) REVERT: E 65 GLU cc_start: 0.9437 (tp30) cc_final: 0.8928 (tp30) REVERT: E 66 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8278 (mmmt) REVERT: E 71 MET cc_start: 0.9008 (mmm) cc_final: 0.8414 (tpt) REVERT: E 95 PHE cc_start: 0.9273 (t80) cc_final: 0.8827 (t80) REVERT: E 112 ARG cc_start: 0.9125 (mtp85) cc_final: 0.8773 (mtp85) REVERT: E 126 LYS cc_start: 0.9162 (tptt) cc_final: 0.8738 (tppt) REVERT: F 5 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8489 (mm-30) REVERT: F 88 MET cc_start: 0.8158 (tpp) cc_final: 0.7882 (tpp) REVERT: F 90 MET cc_start: 0.8611 (mpp) cc_final: 0.8109 (mpp) REVERT: H 43 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8472 (tp30) REVERT: H 80 ARG cc_start: 0.9091 (mtp-110) cc_final: 0.8577 (mtp-110) REVERT: H 85 ILE cc_start: 0.9465 (mm) cc_final: 0.9117 (mm) REVERT: H 86 TYR cc_start: 0.8612 (m-80) cc_final: 0.7591 (m-80) REVERT: H 96 MET cc_start: 0.9203 (mtm) cc_final: 0.8967 (ptp) REVERT: H 124 GLU cc_start: 0.9317 (tt0) cc_final: 0.8521 (tt0) REVERT: H 128 TYR cc_start: 0.8958 (m-80) cc_final: 0.8489 (m-80) REVERT: K 42 LEU cc_start: 0.8792 (mm) cc_final: 0.8409 (mm) REVERT: L 5 ASN cc_start: 0.9576 (t0) cc_final: 0.9168 (t0) REVERT: L 90 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8676 (mm) REVERT: O 59 MET cc_start: 0.9113 (mmp) cc_final: 0.7477 (mmp) REVERT: O 65 LYS cc_start: 0.9673 (mtpt) cc_final: 0.9382 (ptpp) REVERT: P 1 MET cc_start: 0.8722 (pmm) cc_final: 0.8470 (pmm) REVERT: P 26 ASN cc_start: 0.9010 (m110) cc_final: 0.8694 (m110) REVERT: P 53 ASP cc_start: 0.9258 (t0) cc_final: 0.8882 (t0) REVERT: Q 34 TYR cc_start: 0.9390 (m-80) cc_final: 0.9125 (m-10) REVERT: Q 80 GLU cc_start: 0.8878 (tp30) cc_final: 0.8477 (tm-30) REVERT: T 13 GLN cc_start: 0.9473 (pt0) cc_final: 0.9066 (pp30) REVERT: T 54 MET cc_start: 0.8555 (tpp) cc_final: 0.8161 (tpt) REVERT: U 23 CYS cc_start: 0.8765 (p) cc_final: 0.8364 (p) REVERT: U 35 ARG cc_start: 0.8994 (ttm170) cc_final: 0.8630 (mmt90) REVERT: U 36 GLU cc_start: 0.9752 (tp30) cc_final: 0.9316 (tp30) REVERT: U 40 LYS cc_start: 0.9549 (mtpt) cc_final: 0.9065 (mtpt) REVERT: X 108 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7698 (tp-100) REVERT: X 145 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8396 (t0) REVERT: Y 104 MET cc_start: 0.7350 (tmm) cc_final: 0.7088 (ppp) REVERT: Y 116 TYR cc_start: 0.7699 (m-80) cc_final: 0.6745 (m-80) REVERT: Y 136 MET cc_start: 0.8492 (mpt) cc_final: 0.8253 (mpp) REVERT: Y 163 MET cc_start: 0.9613 (mmm) cc_final: 0.9198 (mmm) REVERT: Y 241 MET cc_start: 0.9384 (mmm) cc_final: 0.9015 (mmm) REVERT: Y 247 MET cc_start: 0.9265 (mtm) cc_final: 0.8910 (mtp) outliers start: 43 outliers final: 36 residues processed: 355 average time/residue: 0.2290 time to fit residues: 125.7791 Evaluate side-chains 355 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 316 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 108 GLN Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 226 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [225, 30, 55, 48, 94, 87, 143, 7, 192, 23, 200] chunk 225 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 55 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 143 optimal weight: 5.9990 chunk 7 optimal weight: 30.0000 chunk 192 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 200 optimal weight: 0.8980 overall best weight: 8.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 GLN E 121 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.024295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.019201 restraints weight = 454181.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.019972 restraints weight = 180427.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.020444 restraints weight = 105219.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.020740 restraints weight = 75184.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.020905 restraints weight = 61379.711| |-----------------------------------------------------------------------------| r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36819 Z= 0.301 Angle : 0.751 21.317 54562 Z= 0.407 Chirality : 0.045 0.341 6894 Planarity : 0.006 0.051 3326 Dihedral : 23.937 179.365 17103 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 29.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.06 % Allowed : 28.30 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1660 helix: -0.64 (0.18), residues: 697 sheet: -1.36 (0.28), residues: 312 loop : -0.84 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG O 63 TYR 0.034 0.003 TYR D 76 PHE 0.019 0.002 PHE H 66 TRP 0.010 0.002 TRP D 170 HIS 0.010 0.002 HIS P 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.30 (36819) covalent geometry : angle 0.75055 / 0.41 (54562) hydrogen bonds : bond 0.10210 / 10.97 ( 1506) hydrogen bonds : angle 4.82417 / 6.19 ( 3181) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 310 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7654 (t80) cc_final: 0.7252 (t80) REVERT: D 75 TYR cc_start: 0.9376 (m-80) cc_final: 0.8799 (m-80) REVERT: D 178 MET cc_start: 0.8740 (ptp) cc_final: 0.8508 (pmm) REVERT: D 182 PHE cc_start: 0.9131 (t80) cc_final: 0.8824 (t80) REVERT: D 196 ASN cc_start: 0.9122 (m-40) cc_final: 0.8689 (m110) REVERT: E 12 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8382 (tm-30) REVERT: E 16 ILE cc_start: 0.9563 (tp) cc_final: 0.9317 (mp) REVERT: E 30 ILE cc_start: 0.8552 (mm) cc_final: 0.8247 (mm) REVERT: E 54 ARG cc_start: 0.9018 (mmm160) cc_final: 0.8690 (mpt180) REVERT: E 62 LYS cc_start: 0.7293 (mmmm) cc_final: 0.7014 (mtmm) REVERT: E 65 GLU cc_start: 0.9426 (tp30) cc_final: 0.9114 (tp30) REVERT: E 66 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8330 (mmmt) REVERT: E 68 ARG cc_start: 0.9174 (ptp-110) cc_final: 0.8567 (ptp90) REVERT: E 71 MET cc_start: 0.8960 (mmm) cc_final: 0.8402 (tpt) REVERT: E 95 PHE cc_start: 0.9269 (t80) cc_final: 0.8843 (t80) REVERT: E 112 ARG cc_start: 0.9140 (mtp85) cc_final: 0.8739 (mtp85) REVERT: E 126 LYS cc_start: 0.9228 (tptt) cc_final: 0.8756 (tppt) REVERT: E 147 MET cc_start: 0.8036 (tpt) cc_final: 0.7749 (tpt) REVERT: F 8 PHE cc_start: 0.9715 (p90) cc_final: 0.9164 (p90) REVERT: F 88 MET cc_start: 0.8245 (tpp) cc_final: 0.7926 (tpp) REVERT: F 90 MET cc_start: 0.8600 (mpp) cc_final: 0.8270 (mpp) REVERT: H 43 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8866 (tp30) REVERT: H 80 ARG cc_start: 0.9084 (mtp-110) cc_final: 0.8747 (mtp180) REVERT: H 85 ILE cc_start: 0.9472 (mm) cc_final: 0.9154 (mp) REVERT: H 86 TYR cc_start: 0.8631 (m-80) cc_final: 0.7427 (m-80) REVERT: H 124 GLU cc_start: 0.9311 (tt0) cc_final: 0.8300 (tt0) REVERT: H 128 TYR cc_start: 0.8974 (m-80) cc_final: 0.8566 (m-80) REVERT: K 42 LEU cc_start: 0.8777 (mm) cc_final: 0.8416 (mm) REVERT: K 125 LYS cc_start: 0.9415 (ptpt) cc_final: 0.8925 (ptpt) REVERT: L 5 ASN cc_start: 0.9574 (t0) cc_final: 0.9200 (t0) REVERT: L 7 LEU cc_start: 0.9866 (mm) cc_final: 0.9589 (mp) REVERT: L 90 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8633 (mm) REVERT: O 59 MET cc_start: 0.9417 (mmp) cc_final: 0.8978 (mmm) REVERT: O 65 LYS cc_start: 0.9671 (mtpt) cc_final: 0.9450 (ptpp) REVERT: P 1 MET cc_start: 0.8707 (pmm) cc_final: 0.8393 (pmm) REVERT: P 53 ASP cc_start: 0.9289 (t0) cc_final: 0.8924 (t0) REVERT: Q 34 TYR cc_start: 0.9382 (m-80) cc_final: 0.9119 (m-10) REVERT: Q 80 GLU cc_start: 0.8872 (tp30) cc_final: 0.8426 (tm-30) REVERT: T 13 GLN cc_start: 0.9551 (pt0) cc_final: 0.9105 (pp30) REVERT: T 54 MET cc_start: 0.8568 (tpp) cc_final: 0.8196 (tpt) REVERT: U 23 CYS cc_start: 0.8870 (p) cc_final: 0.8487 (p) REVERT: U 35 ARG cc_start: 0.9014 (ttm170) cc_final: 0.8761 (mtt180) REVERT: U 36 GLU cc_start: 0.9748 (tp30) cc_final: 0.9281 (tp30) REVERT: U 40 LYS cc_start: 0.9494 (mtpt) cc_final: 0.8851 (mtpt) REVERT: X 108 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7942 (tp40) REVERT: X 145 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8163 (t0) REVERT: Y 104 MET cc_start: 0.7624 (tmm) cc_final: 0.7358 (ppp) REVERT: Y 116 TYR cc_start: 0.7764 (m-80) cc_final: 0.6769 (m-80) REVERT: Y 136 MET cc_start: 0.8607 (mpt) cc_final: 0.8404 (mpp) REVERT: Y 163 MET cc_start: 0.9601 (mmm) cc_final: 0.9178 (mmm) REVERT: Y 241 MET cc_start: 0.9430 (mmm) cc_final: 0.9055 (mmm) REVERT: Y 247 MET cc_start: 0.9249 (mtm) cc_final: 0.8838 (mtp) outliers start: 43 outliers final: 36 residues processed: 336 average time/residue: 0.2351 time to fit residues: 122.2980 Evaluate side-chains 341 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 108 GLN Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 226 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [152, 159, 10, 73, 127, 84, 176, 200, 55, 238, 244] chunk 152 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 176 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.024347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.019235 restraints weight = 455062.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.020011 restraints weight = 180861.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.020479 restraints weight = 105340.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.020772 restraints weight = 75887.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.020925 restraints weight = 61640.253| |-----------------------------------------------------------------------------| r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.195 36819 Z= 0.300 Angle : 0.823 59.193 54562 Z= 0.462 Chirality : 0.044 0.339 6894 Planarity : 0.006 0.059 3326 Dihedral : 23.942 179.371 17103 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 30.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.06 % Allowed : 28.65 % Favored : 68.28 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.20), residues: 1660 helix: -0.65 (0.18), residues: 697 sheet: -1.38 (0.28), residues: 312 loop : -0.86 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG X 93 TYR 0.027 0.003 TYR D 76 PHE 0.050 0.002 PHE X 94 TRP 0.009 0.002 TRP D 170 HIS 0.038 0.003 HIS U 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.30 (36819) covalent geometry : angle 0.82258 / 0.46 (54562) hydrogen bonds : bond 0.10246 / 11.02 ( 1506) hydrogen bonds : angle 4.83301 / 6.20 ( 3181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5622.89 seconds wall clock time: 98 minutes 35.68 seconds (5915.68 seconds total)