Starting phenix.real_space_refine on Thu Jul 2 20:23:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9umz_64333/07_2026/9umz_64333.cif Found real_map, /net/cci-nas-00/data/ceres_data/9umz_64333/07_2026/9umz_64333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9umz_64333/07_2026/9umz_64333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9umz_64333/07_2026/9umz_64333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9umz_64333/07_2026/9umz_64333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9umz_64333/07_2026/9umz_64333.map" } resolution = 3.98 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 54 5.16 5 C 6294 2.51 5 N 1664 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10018 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1886 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 232} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1895 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "C" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1895 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "D" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1895 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "E" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1887 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "K" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 560 Classifications: {'RNA': 28} Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 22} Link IDs: {'rna2p': 5, 'rna3p': 22} Time building chain proxies: 1.92, per 1000 atoms: 0.19 Number of scatterers: 10018 At special positions: 0 Unit cell: (71.25, 110.2, 120.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 28 15.00 O 1978 8.00 N 1664 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS E 116 " - pdb=" SG CYS E 146 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 348.9 milliseconds 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 0 sheets defined 74.3% alpha, 0.0% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 17 through 28 Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.688A pdb=" N ILE A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 64 removed outlier: 3.659A pdb=" N LYS A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 removed outlier: 3.641A pdb=" N GLY A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.569A pdb=" N ARG A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.550A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 removed outlier: 4.378A pdb=" N ALA A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 147 through 152 removed outlier: 4.101A pdb=" N GLY A 150 " --> pdb=" O MET A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 182 removed outlier: 3.585A pdb=" N TRP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 197 through 206 removed outlier: 3.623A pdb=" N LEU A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.975A pdb=" N ARG A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.552A pdb=" N GLU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 4.094A pdb=" N PHE B 11 " --> pdb=" O ILE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.702A pdb=" N ARG B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 22 through 27' Processing helix chain 'B' and resid 36 through 47 removed outlier: 3.632A pdb=" N LYS B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 64 removed outlier: 3.710A pdb=" N LYS B 55 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.575A pdb=" N ALA B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.586A pdb=" N THR B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.851A pdb=" N MET B 145 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 159 through 182 removed outlier: 4.191A pdb=" N TRP B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 174 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 207 removed outlier: 3.960A pdb=" N PHE B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix removed outlier: 3.510A pdb=" N ALA B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.613A pdb=" N LYS B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.680A pdb=" N GLU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.726A pdb=" N ARG C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 29 Processing helix chain 'C' and resid 34 through 46 removed outlier: 3.561A pdb=" N THR C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 64 removed outlier: 4.240A pdb=" N VAL C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 76 through 91 removed outlier: 4.034A pdb=" N ARG C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.639A pdb=" N LEU C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 removed outlier: 3.529A pdb=" N ALA C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 159 through 182 removed outlier: 3.903A pdb=" N TRP C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 186 removed outlier: 3.550A pdb=" N ARG C 186 " --> pdb=" O VAL C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 186' Processing helix chain 'C' and resid 189 through 197 removed outlier: 3.653A pdb=" N ASN C 195 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.592A pdb=" N ARG C 215 " --> pdb=" O PRO C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 244 removed outlier: 4.079A pdb=" N GLU C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 14 removed outlier: 3.735A pdb=" N ARG D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN D 14 " --> pdb=" O GLU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 34 through 47 removed outlier: 3.515A pdb=" N LEU D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 64 removed outlier: 4.162A pdb=" N LYS D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.778A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 103 through 111 Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 123 through 126 removed outlier: 3.721A pdb=" N LEU D 126 " --> pdb=" O LYS D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 123 through 126' Processing helix chain 'D' and resid 129 through 137 removed outlier: 3.652A pdb=" N LEU D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 removed outlier: 3.602A pdb=" N PHE D 149 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 150 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 151 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 182 removed outlier: 3.641A pdb=" N THR D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 206 removed outlier: 3.966A pdb=" N PHE D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) Proline residue: D 200 - end of helix Processing helix chain 'D' and resid 211 through 222 removed outlier: 3.700A pdb=" N LYS D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 244 removed outlier: 3.609A pdb=" N ASN D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.700A pdb=" N ALA E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 14 " --> pdb=" O GLU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 29 removed outlier: 3.552A pdb=" N GLU E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 46 removed outlier: 3.514A pdb=" N ILE E 38 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 64 removed outlier: 3.963A pdb=" N LYS E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.557A pdb=" N GLY E 73 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 91 removed outlier: 3.701A pdb=" N ARG E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.588A pdb=" N ALA E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA E 120 " --> pdb=" O CYS E 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 141 through 145 removed outlier: 3.549A pdb=" N MET E 144 " --> pdb=" O PRO E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 159 through 182 removed outlier: 3.715A pdb=" N LEU E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN E 174 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 196 Processing helix chain 'E' and resid 197 through 207 removed outlier: 3.512A pdb=" N ALA E 203 " --> pdb=" O ASP E 199 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 204 " --> pdb=" O PRO E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 222 removed outlier: 3.588A pdb=" N VAL E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 244 removed outlier: 3.663A pdb=" N GLU E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3069 1.34 - 1.46: 1603 1.46 - 1.58: 5436 1.58 - 1.70: 55 1.70 - 1.82: 98 Bond restraints: 10261 Sorted by residual: bond pdb=" CA GLU B 31 " pdb=" CB GLU B 31 " ideal model delta sigma weight residual 1.526 1.556 -0.030 1.70e-02 3.46e+03 3.15e+00 bond pdb=" CG ARG B 26 " pdb=" CD ARG B 26 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CB GLU E 88 " pdb=" CG GLU E 88 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.20e-01 bond pdb=" CB GLN D 87 " pdb=" CG GLN D 87 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.74e-01 bond pdb=" C GLY D 79 " pdb=" O GLY D 79 " ideal model delta sigma weight residual 1.239 1.245 -0.006 7.10e-03 1.98e+04 7.71e-01 ... (remaining 10256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 13744 1.75 - 3.50: 208 3.50 - 5.25: 41 5.25 - 7.00: 8 7.00 - 8.74: 6 Bond angle restraints: 14007 Sorted by residual: angle pdb=" C GLU A 138 " pdb=" N ASN A 139 " pdb=" CA ASN A 139 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.24e+00 angle pdb=" CB MET D 133 " pdb=" CG MET D 133 " pdb=" SD MET D 133 " ideal model delta sigma weight residual 112.70 121.44 -8.74 3.00e+00 1.11e-01 8.50e+00 angle pdb=" CB MET A 167 " pdb=" CG MET A 167 " pdb=" SD MET A 167 " ideal model delta sigma weight residual 112.70 121.15 -8.45 3.00e+00 1.11e-01 7.94e+00 angle pdb=" CB MET C 84 " pdb=" CG MET C 84 " pdb=" SD MET C 84 " ideal model delta sigma weight residual 112.70 121.05 -8.35 3.00e+00 1.11e-01 7.75e+00 angle pdb=" CA LYS B 89 " pdb=" CB LYS B 89 " pdb=" CG LYS B 89 " ideal model delta sigma weight residual 114.10 119.54 -5.44 2.00e+00 2.50e-01 7.41e+00 ... (remaining 14002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5651 17.96 - 35.92: 523 35.92 - 53.88: 104 53.88 - 71.84: 44 71.84 - 89.81: 11 Dihedral angle restraints: 6333 sinusoidal: 2781 harmonic: 3552 Sorted by residual: dihedral pdb=" CA TYR B 30 " pdb=" C TYR B 30 " pdb=" N GLU B 31 " pdb=" CA GLU B 31 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP E 34 " pdb=" CB ASP E 34 " pdb=" CG ASP E 34 " pdb=" OD1 ASP E 34 " ideal model delta sinusoidal sigma weight residual -30.00 -91.00 61.00 1 2.00e+01 2.50e-03 1.24e+01 dihedral pdb=" CB GLU D 20 " pdb=" CG GLU D 20 " pdb=" CD GLU D 20 " pdb=" OE1 GLU D 20 " ideal model delta sinusoidal sigma weight residual 0.00 88.34 -88.34 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 6330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1420 0.057 - 0.114: 190 0.114 - 0.171: 13 0.171 - 0.228: 0 0.228 - 0.285: 1 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CB ILE A 102 " pdb=" CA ILE A 102 " pdb=" CG1 ILE A 102 " pdb=" CG2 ILE A 102 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA VAL A 158 " pdb=" N VAL A 158 " pdb=" C VAL A 158 " pdb=" CB VAL A 158 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE D 153 " pdb=" N ILE D 153 " pdb=" C ILE D 153 " pdb=" CB ILE D 153 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1621 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 141 " 0.029 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO C 142 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 26 " -0.123 9.50e-02 1.11e+02 5.55e-02 2.52e+00 pdb=" NE ARG B 26 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 26 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 26 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 26 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 111 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO E 112 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " -0.022 5.00e-02 4.00e+02 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 174 2.67 - 3.23: 10148 3.23 - 3.79: 15803 3.79 - 4.34: 20710 4.34 - 4.90: 32153 Nonbonded interactions: 78988 Sorted by model distance: nonbonded pdb=" O LEU C 28 " pdb=" NH2 ARG D 64 " model vdw 2.114 3.120 nonbonded pdb=" OE2 GLU A 27 " pdb=" OG SER B 78 " model vdw 2.173 3.040 nonbonded pdb=" OD2 ASP C 199 " pdb=" O2' U K 15 " model vdw 2.189 3.040 nonbonded pdb=" O THR D 98 " pdb=" OG SER D 101 " model vdw 2.219 3.040 nonbonded pdb=" O SER E 159 " pdb=" OG1 THR E 162 " model vdw 2.237 3.040 ... (remaining 78983 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 245) selection = (chain 'B' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 245)) selection = (chain 'C' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 245)) selection = (chain 'D' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 245)) selection = (chain 'E' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 245)) } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.300 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 : 0.002 0.034 10263 Z= 0.109 Angle : 0.570 8.745 14011 Z= 0.287 Chirality : 0.038 0.285 1624 Planarity : 0.004 0.056 1686 Dihedral : 15.104 89.806 4029 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.23), residues: 1214 helix: -0.49 (0.18), residues: 745 sheet: None (None), residues: 0 loop : 0.38 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 26 TYR 0.021 0.001 TYR B 170 PHE 0.023 0.002 PHE E 197 TRP 0.023 0.002 TRP C 114 HIS 0.001 0.000 HIS D 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10261) covalent geometry : angle 0.56940 / 0.29 (14007) SS BOND : bond 0.00306 / 0.16 ( 2) SS BOND : angle 1.16625 / 0.63 ( 4) hydrogen bonds : bond 0.29379 / 18.59 ( 496) hydrogen bonds : angle 8.06804 / 5.60 ( 1434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7960 (tpp80) REVERT: B 134 ASN cc_start: 0.8791 (m110) cc_final: 0.8579 (m-40) REVERT: E 144 MET cc_start: 0.7805 (ppp) cc_final: 0.7318 (ppp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.0769 time to fit residues: 26.8040 Evaluate side-chains 199 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN A 244 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS C 212 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.182554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.154295 restraints weight = 16841.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.159020 restraints weight = 10507.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.162421 restraints weight = 7434.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.164845 restraints weight = 5694.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.166645 restraints weight = 4624.697| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10263 Z= 0.156 Angle : 0.632 8.468 14011 Z= 0.331 Chirality : 0.042 0.158 1624 Planarity : 0.005 0.044 1686 Dihedral : 12.222 77.866 1759 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.70 % Allowed : 12.53 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.23), residues: 1214 helix: -0.36 (0.17), residues: 788 sheet: None (None), residues: 0 loop : 0.13 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 26 TYR 0.016 0.002 TYR A 194 PHE 0.026 0.002 PHE B 11 TRP 0.017 0.002 TRP D 50 HIS 0.002 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (10261) covalent geometry : angle 0.63115 / 0.33 (14007) SS BOND : bond 0.00386 / 0.20 ( 2) SS BOND : angle 1.61957 / 0.89 ( 4) hydrogen bonds : bond 0.05209 / 3.32 ( 496) hydrogen bonds : angle 5.32440 / 3.69 ( 1434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.340 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: A 144 MET cc_start: 0.7332 (ttm) cc_final: 0.7077 (ttm) REVERT: B 17 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7364 (p0) REVERT: B 116 CYS cc_start: 0.7522 (m) cc_final: 0.7298 (m) REVERT: B 134 ASN cc_start: 0.8821 (m110) cc_final: 0.8572 (m-40) REVERT: B 174 GLN cc_start: 0.8573 (mp10) cc_final: 0.8315 (mp10) REVERT: C 17 ASN cc_start: 0.8586 (t0) cc_final: 0.8302 (t0) REVERT: E 144 MET cc_start: 0.7885 (ppp) cc_final: 0.7164 (ppp) outliers start: 17 outliers final: 5 residues processed: 226 average time/residue: 0.0783 time to fit residues: 25.1950 Evaluate side-chains 202 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain C residue 193 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 182 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** E 212 ASN ** 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 = 0.3934 r_free = 0.3934 target = 0.157254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127126 restraints weight = 16931.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131387 restraints weight = 10898.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134451 restraints weight = 7945.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136659 restraints weight = 6272.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138048 restraints weight = 5240.866| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 10263 Z= 0.285 Angle : 0.750 9.773 14011 Z= 0.392 Chirality : 0.047 0.181 1624 Planarity : 0.005 0.056 1686 Dihedral : 12.726 82.472 1759 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.21 % Allowed : 16.43 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1214 helix: -0.42 (0.17), residues: 782 sheet: None (None), residues: 0 loop : -0.07 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 95 TYR 0.021 0.003 TYR A 194 PHE 0.023 0.004 PHE B 210 TRP 0.020 0.003 TRP D 114 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.28 (10261) covalent geometry : angle 0.74965 / 0.39 (14007) SS BOND : bond 0.00530 / 0.28 ( 2) SS BOND : angle 1.83147 / 1.00 ( 4) hydrogen bonds : bond 0.05207 / 3.30 ( 496) hydrogen bonds : angle 5.43348 / 3.72 ( 1434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8337 (t80) cc_final: 0.7833 (t80) REVERT: A 144 MET cc_start: 0.7395 (ttm) cc_final: 0.6816 (ttm) REVERT: A 185 MET cc_start: 0.8900 (mmt) cc_final: 0.8530 (mpp) REVERT: A 195 ASN cc_start: 0.8368 (m110) cc_final: 0.6987 (m110) REVERT: A 198 ARG cc_start: 0.7698 (mpp80) cc_final: 0.7497 (mpp80) REVERT: A 217 LYS cc_start: 0.9021 (pttm) cc_final: 0.8739 (pttp) REVERT: B 88 GLU cc_start: 0.8055 (tt0) cc_final: 0.7827 (tm-30) REVERT: B 134 ASN cc_start: 0.8832 (m110) cc_final: 0.8568 (m-40) REVERT: C 17 ASN cc_start: 0.8704 (t0) cc_final: 0.8363 (t0) REVERT: C 26 ARG cc_start: 0.8870 (mtm180) cc_final: 0.8646 (ttp-110) REVERT: C 133 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7125 (ttp) REVERT: C 213 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8227 (p0) REVERT: D 100 LEU cc_start: 0.8433 (tp) cc_final: 0.8075 (tp) REVERT: D 147 MET cc_start: 0.8397 (tpt) cc_final: 0.7860 (tpt) REVERT: D 168 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6803 (mt-10) REVERT: E 75 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5665 (ttt) REVERT: E 144 MET cc_start: 0.7920 (ppp) cc_final: 0.7102 (ppp) REVERT: E 220 LYS cc_start: 0.8116 (mmtp) cc_final: 0.7861 (mmtp) REVERT: E 242 TYR cc_start: 0.7571 (t80) cc_final: 0.7233 (t80) outliers start: 42 outliers final: 24 residues processed: 236 average time/residue: 0.0717 time to fit residues: 25.0038 Evaluate side-chains 224 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 193 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.5980 chunk 95 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 17 ASN B 174 GLN B 212 ASN D 182 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.170538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.140546 restraints weight = 16695.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.145348 restraints weight = 10426.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.148800 restraints weight = 7395.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.151293 restraints weight = 5687.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.152905 restraints weight = 4640.734| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10263 Z= 0.134 Angle : 0.610 11.283 14011 Z= 0.312 Chirality : 0.041 0.181 1624 Planarity : 0.004 0.051 1686 Dihedral : 12.567 83.802 1759 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.71 % Allowed : 20.84 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.23), residues: 1214 helix: -0.19 (0.18), residues: 787 sheet: None (None), residues: 0 loop : -0.06 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 233 TYR 0.022 0.002 TYR A 194 PHE 0.029 0.002 PHE B 60 TRP 0.031 0.002 TRP E 173 HIS 0.001 0.001 HIS E 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10261) covalent geometry : angle 0.61005 / 0.31 (14007) SS BOND : bond 0.02483 / 1.20 ( 2) SS BOND : angle 1.37604 / 0.73 ( 4) hydrogen bonds : bond 0.04131 / 2.64 ( 496) hydrogen bonds : angle 4.92939 / 3.39 ( 1434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8119 (t80) cc_final: 0.7457 (t80) REVERT: A 144 MET cc_start: 0.7455 (ttm) cc_final: 0.6537 (ttm) REVERT: A 194 TYR cc_start: 0.6870 (t80) cc_final: 0.6548 (t80) REVERT: A 195 ASN cc_start: 0.8317 (m-40) cc_final: 0.7115 (m-40) REVERT: A 217 LYS cc_start: 0.8997 (pttm) cc_final: 0.8697 (pttp) REVERT: B 88 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: B 134 ASN cc_start: 0.8794 (m110) cc_final: 0.8478 (m-40) REVERT: C 17 ASN cc_start: 0.8596 (t0) cc_final: 0.8366 (t0) REVERT: C 26 ARG cc_start: 0.8808 (mtm180) cc_final: 0.8552 (ttp-110) REVERT: C 219 LEU cc_start: 0.8759 (mt) cc_final: 0.8549 (mt) REVERT: D 100 LEU cc_start: 0.8354 (tp) cc_final: 0.7960 (tt) REVERT: D 125 TYR cc_start: 0.8077 (m-80) cc_final: 0.7794 (m-80) REVERT: D 133 MET cc_start: 0.8134 (mmm) cc_final: 0.7915 (mmm) REVERT: E 144 MET cc_start: 0.7962 (ppp) cc_final: 0.6966 (ppp) REVERT: E 168 GLU cc_start: 0.8866 (tp30) cc_final: 0.8572 (tp30) REVERT: E 242 TYR cc_start: 0.7634 (t80) cc_final: 0.7070 (t80) outliers start: 27 outliers final: 16 residues processed: 235 average time/residue: 0.0758 time to fit residues: 26.0915 Evaluate side-chains 218 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.0030 chunk 49 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** E 212 ASN ** 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 = 0.4036 r_free = 0.4036 target = 0.166606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136443 restraints weight = 16859.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141049 restraints weight = 10582.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144391 restraints weight = 7578.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146537 restraints weight = 5885.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148357 restraints weight = 4905.258| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10263 Z= 0.189 Angle : 0.658 11.264 14011 Z= 0.334 Chirality : 0.042 0.175 1624 Planarity : 0.005 0.098 1686 Dihedral : 12.639 84.947 1759 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.61 % Allowed : 21.54 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1214 helix: -0.17 (0.18), residues: 793 sheet: None (None), residues: 0 loop : -0.19 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 106 TYR 0.037 0.002 TYR A 194 PHE 0.029 0.003 PHE E 197 TRP 0.018 0.002 TRP E 50 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (10261) covalent geometry : angle 0.65814 / 0.33 (14007) SS BOND : bond 0.00364 / 0.19 ( 2) SS BOND : angle 1.20052 / 0.66 ( 4) hydrogen bonds : bond 0.04126 / 2.63 ( 496) hydrogen bonds : angle 4.93991 / 3.39 ( 1434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8157 (t80) cc_final: 0.7537 (t80) REVERT: A 144 MET cc_start: 0.7517 (ttm) cc_final: 0.6620 (ttm) REVERT: A 210 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: A 217 LYS cc_start: 0.8993 (pttm) cc_final: 0.8721 (pttp) REVERT: B 88 GLU cc_start: 0.8126 (tt0) cc_final: 0.7916 (tm-30) REVERT: B 134 ASN cc_start: 0.8806 (m110) cc_final: 0.8499 (m-40) REVERT: B 147 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7358 (tpt) REVERT: C 17 ASN cc_start: 0.8636 (t0) cc_final: 0.8301 (t0) REVERT: C 26 ARG cc_start: 0.8828 (mtm180) cc_final: 0.8568 (ttp-110) REVERT: C 133 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7261 (ttp) REVERT: C 170 TYR cc_start: 0.8422 (t80) cc_final: 0.8070 (t80) REVERT: C 219 LEU cc_start: 0.8805 (mt) cc_final: 0.8575 (mt) REVERT: D 100 LEU cc_start: 0.8381 (tp) cc_final: 0.7974 (tt) REVERT: E 144 MET cc_start: 0.8057 (ppp) cc_final: 0.7151 (ppp) REVERT: E 168 GLU cc_start: 0.8928 (tp30) cc_final: 0.8518 (tp30) REVERT: E 220 LYS cc_start: 0.7945 (mmtp) cc_final: 0.7721 (mmtp) REVERT: E 242 TYR cc_start: 0.7620 (t80) cc_final: 0.6931 (t80) outliers start: 36 outliers final: 25 residues processed: 233 average time/residue: 0.0783 time to fit residues: 26.4392 Evaluate side-chains 226 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 193 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 10 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.0270 chunk 66 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.171890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142087 restraints weight = 16736.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.146926 restraints weight = 10393.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.150383 restraints weight = 7319.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.152825 restraints weight = 5633.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.154600 restraints weight = 4600.792| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10263 Z= 0.125 Angle : 0.627 11.668 14011 Z= 0.314 Chirality : 0.040 0.161 1624 Planarity : 0.004 0.050 1686 Dihedral : 12.596 86.157 1759 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.41 % Allowed : 23.45 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.24), residues: 1214 helix: -0.09 (0.18), residues: 799 sheet: None (None), residues: 0 loop : -0.08 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 233 TYR 0.013 0.002 TYR C 170 PHE 0.029 0.002 PHE E 197 TRP 0.019 0.002 TRP E 173 HIS 0.001 0.001 HIS E 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (10261) covalent geometry : angle 0.62683 / 0.31 (14007) SS BOND : bond 0.00834 / 0.40 ( 2) SS BOND : angle 0.79435 / 0.45 ( 4) hydrogen bonds : bond 0.03797 / 2.44 ( 496) hydrogen bonds : angle 4.77360 / 3.28 ( 1434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.561 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: A 80 SER cc_start: 0.7480 (OUTLIER) cc_final: 0.6883 (p) REVERT: A 140 TYR cc_start: 0.8060 (t80) cc_final: 0.7356 (t80) REVERT: A 144 MET cc_start: 0.7438 (ttm) cc_final: 0.6358 (ttm) REVERT: A 210 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6593 (m-80) REVERT: B 88 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: B 134 ASN cc_start: 0.8744 (m110) cc_final: 0.8440 (m-40) REVERT: B 144 MET cc_start: 0.8328 (mmt) cc_final: 0.8031 (tpp) REVERT: B 225 LEU cc_start: 0.5347 (OUTLIER) cc_final: 0.5001 (mp) REVERT: C 17 ASN cc_start: 0.8593 (t0) cc_final: 0.8323 (t0) REVERT: C 26 ARG cc_start: 0.8775 (mtm180) cc_final: 0.8523 (ttp-110) REVERT: C 95 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7996 (mtp85) REVERT: C 133 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7448 (ttp) REVERT: C 170 TYR cc_start: 0.8446 (t80) cc_final: 0.8114 (t80) REVERT: C 185 MET cc_start: 0.8073 (tpt) cc_final: 0.7748 (tpt) REVERT: D 100 LEU cc_start: 0.8313 (tp) cc_final: 0.7853 (tt) REVERT: D 133 MET cc_start: 0.8116 (mmm) cc_final: 0.7884 (mmm) REVERT: E 75 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.4886 (ttt) REVERT: E 144 MET cc_start: 0.7938 (ppp) cc_final: 0.7009 (ppp) REVERT: E 168 GLU cc_start: 0.8882 (tp30) cc_final: 0.8395 (tp30) REVERT: E 210 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: E 242 TYR cc_start: 0.7584 (t80) cc_final: 0.6867 (t80) outliers start: 34 outliers final: 20 residues processed: 236 average time/residue: 0.0756 time to fit residues: 26.3571 Evaluate side-chains 225 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 212 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** E 212 ASN ** 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 = 0.4088 r_free = 0.4088 target = 0.171369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142002 restraints weight = 16668.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.146744 restraints weight = 10370.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.150124 restraints weight = 7306.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.152471 restraints weight = 5607.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.154323 restraints weight = 4594.993| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10263 Z= 0.137 Angle : 0.620 11.616 14011 Z= 0.313 Chirality : 0.040 0.186 1624 Planarity : 0.004 0.051 1686 Dihedral : 12.580 86.733 1759 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.91 % Allowed : 23.75 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1214 helix: -0.07 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -0.19 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 233 TYR 0.014 0.002 TYR E 170 PHE 0.022 0.002 PHE E 197 TRP 0.023 0.002 TRP D 50 HIS 0.002 0.001 HIS E 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10261) covalent geometry : angle 0.61955 / 0.31 (14007) SS BOND : bond 0.00545 / 0.26 ( 2) SS BOND : angle 2.08404 / 1.07 ( 4) hydrogen bonds : bond 0.03719 / 2.39 ( 496) hydrogen bonds : angle 4.74726 / 3.25 ( 1434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.7490 (OUTLIER) cc_final: 0.6890 (p) REVERT: A 140 TYR cc_start: 0.8032 (t80) cc_final: 0.7300 (t80) REVERT: A 144 MET cc_start: 0.7452 (ttm) cc_final: 0.6338 (ttm) REVERT: A 198 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.6941 (mpp80) REVERT: A 210 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6661 (m-80) REVERT: B 88 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: B 134 ASN cc_start: 0.8844 (m110) cc_final: 0.8540 (m-40) REVERT: B 144 MET cc_start: 0.8286 (mmt) cc_final: 0.8063 (tpp) REVERT: C 26 ARG cc_start: 0.8779 (mtm180) cc_final: 0.8519 (ttp-110) REVERT: C 133 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7457 (ttp) REVERT: C 170 TYR cc_start: 0.8450 (t80) cc_final: 0.8151 (t80) REVERT: D 75 MET cc_start: 0.6972 (ptm) cc_final: 0.6734 (ptt) REVERT: D 87 GLN cc_start: 0.7525 (tp40) cc_final: 0.7289 (tp40) REVERT: D 100 LEU cc_start: 0.8275 (tp) cc_final: 0.7816 (tt) REVERT: E 75 MET cc_start: 0.5314 (ttt) cc_final: 0.4603 (ttt) REVERT: E 144 MET cc_start: 0.7931 (ppp) cc_final: 0.7179 (ppp) REVERT: E 168 GLU cc_start: 0.8882 (tp30) cc_final: 0.8373 (tp30) REVERT: E 210 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: E 242 TYR cc_start: 0.7587 (t80) cc_final: 0.6860 (t80) outliers start: 39 outliers final: 27 residues processed: 225 average time/residue: 0.0652 time to fit residues: 21.5396 Evaluate side-chains 225 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 210 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 76 optimal weight: 5.9990 chunk 99 optimal weight: 0.0870 chunk 49 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 39 optimal weight: 0.0270 chunk 94 optimal weight: 0.2980 chunk 84 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 63 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.1634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.175939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147040 restraints weight = 16604.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.151876 restraints weight = 10236.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.155303 restraints weight = 7153.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.157740 restraints weight = 5458.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.159383 restraints weight = 4426.330| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10263 Z= 0.122 Angle : 0.630 12.176 14011 Z= 0.315 Chirality : 0.041 0.369 1624 Planarity : 0.004 0.051 1686 Dihedral : 12.542 87.427 1759 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.81 % Allowed : 25.25 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.23), residues: 1214 helix: -0.10 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -0.11 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 233 TYR 0.025 0.002 TYR A 194 PHE 0.031 0.002 PHE D 149 TRP 0.023 0.002 TRP D 50 HIS 0.001 0.000 HIS D 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10261) covalent geometry : angle 0.62894 / 0.31 (14007) SS BOND : bond 0.00208 / 0.10 ( 2) SS BOND : angle 1.92477 / 0.98 ( 4) hydrogen bonds : bond 0.03638 / 2.34 ( 496) hydrogen bonds : angle 4.67437 / 3.21 ( 1434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.312 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: A 80 SER cc_start: 0.7445 (OUTLIER) cc_final: 0.6825 (p) REVERT: A 140 TYR cc_start: 0.7928 (t80) cc_final: 0.7098 (t80) REVERT: A 144 MET cc_start: 0.7318 (ttm) cc_final: 0.6254 (ttm) REVERT: A 210 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6611 (m-80) REVERT: B 88 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: B 134 ASN cc_start: 0.8808 (m110) cc_final: 0.8503 (m-40) REVERT: C 26 ARG cc_start: 0.8745 (mtm180) cc_final: 0.8501 (ttp-110) REVERT: C 133 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7428 (ttp) REVERT: C 170 TYR cc_start: 0.8442 (t80) cc_final: 0.8159 (t80) REVERT: C 182 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.6995 (t0) REVERT: C 185 MET cc_start: 0.7860 (tpt) cc_final: 0.7641 (tpt) REVERT: D 87 GLN cc_start: 0.7414 (tp40) cc_final: 0.7207 (tp40) REVERT: D 100 LEU cc_start: 0.8254 (tp) cc_final: 0.7765 (tt) REVERT: E 75 MET cc_start: 0.4863 (ttt) cc_final: 0.4132 (ttt) REVERT: E 94 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6667 (mm-30) REVERT: E 144 MET cc_start: 0.7843 (ppp) cc_final: 0.7266 (ppp) REVERT: E 168 GLU cc_start: 0.8869 (tp30) cc_final: 0.8372 (tp30) REVERT: E 210 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: E 242 TYR cc_start: 0.7733 (t80) cc_final: 0.7047 (t80) outliers start: 28 outliers final: 18 residues processed: 228 average time/residue: 0.0686 time to fit residues: 23.1648 Evaluate side-chains 223 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 210 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN E 174 GLN ** E 212 ASN ** 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 = 0.4102 r_free = 0.4102 target = 0.172292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143126 restraints weight = 16777.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.147749 restraints weight = 10507.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.151061 restraints weight = 7481.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.153355 restraints weight = 5776.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155031 restraints weight = 4763.758| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10263 Z= 0.145 Angle : 0.644 11.728 14011 Z= 0.322 Chirality : 0.041 0.215 1624 Planarity : 0.004 0.051 1686 Dihedral : 12.510 89.040 1759 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.21 % Allowed : 25.25 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1214 helix: -0.04 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -0.01 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 233 TYR 0.028 0.002 TYR D 242 PHE 0.029 0.002 PHE A 11 TRP 0.021 0.002 TRP E 4 HIS 0.001 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (10261) covalent geometry : angle 0.64358 / 0.32 (14007) SS BOND : bond 0.00242 / 0.12 ( 2) SS BOND : angle 1.90013 / 0.99 ( 4) hydrogen bonds : bond 0.03642 / 2.34 ( 496) hydrogen bonds : angle 4.66139 / 3.20 ( 1434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.331 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: A 80 SER cc_start: 0.7503 (OUTLIER) cc_final: 0.6906 (p) REVERT: A 140 TYR cc_start: 0.7987 (t80) cc_final: 0.7251 (t80) REVERT: A 144 MET cc_start: 0.7453 (ttm) cc_final: 0.6429 (ttm) REVERT: A 210 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: B 88 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: B 134 ASN cc_start: 0.8849 (m110) cc_final: 0.8553 (m-40) REVERT: C 26 ARG cc_start: 0.8784 (mtm180) cc_final: 0.8533 (ttp-110) REVERT: C 133 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7444 (ttp) REVERT: C 170 TYR cc_start: 0.8456 (t80) cc_final: 0.8237 (t80) REVERT: C 182 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.7226 (t0) REVERT: D 87 GLN cc_start: 0.7478 (tp40) cc_final: 0.7228 (tp40) REVERT: D 100 LEU cc_start: 0.8253 (tp) cc_final: 0.7780 (tt) REVERT: D 144 MET cc_start: 0.5063 (tmm) cc_final: 0.4209 (tmm) REVERT: E 75 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4411 (ttt) REVERT: E 144 MET cc_start: 0.7884 (ppp) cc_final: 0.7307 (ppp) REVERT: E 168 GLU cc_start: 0.8892 (tp30) cc_final: 0.8572 (tp30) REVERT: E 210 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: E 242 TYR cc_start: 0.7739 (t80) cc_final: 0.7203 (t80) outliers start: 32 outliers final: 23 residues processed: 220 average time/residue: 0.0773 time to fit residues: 24.8719 Evaluate side-chains 229 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 210 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.0070 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** E 212 ASN ** 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 = 0.4105 r_free = 0.4105 target = 0.172509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142864 restraints weight = 16619.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.147564 restraints weight = 10356.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.150888 restraints weight = 7342.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.153227 restraints weight = 5681.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.154956 restraints weight = 4673.136| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10263 Z= 0.147 Angle : 0.657 12.374 14011 Z= 0.326 Chirality : 0.041 0.275 1624 Planarity : 0.004 0.052 1686 Dihedral : 12.518 89.544 1759 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.11 % Allowed : 25.55 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1214 helix: -0.03 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -0.01 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 233 TYR 0.026 0.002 TYR A 194 PHE 0.028 0.002 PHE A 11 TRP 0.030 0.002 TRP C 173 HIS 0.001 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10261) covalent geometry : angle 0.65605 / 0.33 (14007) SS BOND : bond 0.00231 / 0.12 ( 2) SS BOND : angle 1.83149 / 0.96 ( 4) hydrogen bonds : bond 0.03673 / 2.35 ( 496) hydrogen bonds : angle 4.64437 / 3.20 ( 1434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.7411 (OUTLIER) cc_final: 0.6830 (p) REVERT: A 140 TYR cc_start: 0.7984 (t80) cc_final: 0.7267 (t80) REVERT: A 144 MET cc_start: 0.7435 (ttm) cc_final: 0.6426 (ttm) REVERT: A 210 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: B 134 ASN cc_start: 0.8841 (m110) cc_final: 0.8546 (m-40) REVERT: B 144 MET cc_start: 0.8418 (mmt) cc_final: 0.8209 (tpp) REVERT: C 26 ARG cc_start: 0.8805 (mtm180) cc_final: 0.8560 (ttp-110) REVERT: C 133 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7502 (ttp) REVERT: C 170 TYR cc_start: 0.8501 (t80) cc_final: 0.8276 (t80) REVERT: D 87 GLN cc_start: 0.7499 (tp40) cc_final: 0.7207 (tp40) REVERT: D 100 LEU cc_start: 0.8292 (tp) cc_final: 0.7827 (tt) REVERT: E 75 MET cc_start: 0.5252 (OUTLIER) cc_final: 0.4476 (ttt) REVERT: E 144 MET cc_start: 0.8058 (ppp) cc_final: 0.7486 (ppp) REVERT: E 168 GLU cc_start: 0.8889 (tp30) cc_final: 0.8612 (tp30) REVERT: E 210 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: E 242 TYR cc_start: 0.7740 (t80) cc_final: 0.7206 (t80) outliers start: 31 outliers final: 23 residues processed: 218 average time/residue: 0.0717 time to fit residues: 23.0248 Evaluate side-chains 223 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 210 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 105 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN E 182 ASN ** E 212 ASN ** 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 = 0.4061 r_free = 0.4061 target = 0.168230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137421 restraints weight = 16903.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142084 restraints weight = 10765.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.145391 restraints weight = 7730.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.147714 restraints weight = 6075.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149001 restraints weight = 5059.466| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 10263 Z= 0.202 Angle : 0.704 12.431 14011 Z= 0.353 Chirality : 0.043 0.182 1624 Planarity : 0.005 0.051 1686 Dihedral : 12.651 89.828 1759 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.21 % Allowed : 25.75 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1214 helix: -0.10 (0.18), residues: 789 sheet: None (None), residues: 0 loop : -0.05 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 233 TYR 0.025 0.002 TYR A 194 PHE 0.026 0.003 PHE A 11 TRP 0.038 0.002 TRP E 4 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (10261) covalent geometry : angle 0.70359 / 0.35 (14007) SS BOND : bond 0.00206 / 0.11 ( 2) SS BOND : angle 1.98850 / 1.05 ( 4) hydrogen bonds : bond 0.03921 / 2.52 ( 496) hydrogen bonds : angle 4.82268 / 3.31 ( 1434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1431.03 seconds wall clock time: 25 minutes 35.09 seconds (1535.09 seconds total)