Starting phenix.real_space_refine on Tue Oct 27 01:41:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36ht_77585/10_2026/36ht_77585.cif Found real_map, /net/cci-nas-00/data/ceres_data/36ht_77585/10_2026/36ht_77585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36ht_77585/10_2026/36ht_77585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36ht_77585/10_2026/36ht_77585.map" model { file = "/net/cci-nas-00/data/ceres_data/36ht_77585/10_2026/36ht_77585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36ht_77585/10_2026/36ht_77585.cif" } resolution = 3.7 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= 0.008 sd= 1.195 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 339 5.49 5 S 49 5.16 5 C 13355 2.51 5 N 3996 2.21 5 O 5038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22777 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2643 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain: "B" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1960 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 234} Chain: "C" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1375 Classifications: {'DNA': 67} Link IDs: {'rna3p': 66} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 9, 'rna3p': 27} Chain: "E" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2643 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain: "G" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1375 Classifications: {'DNA': 67} Link IDs: {'rna3p': 66} Chain: "H" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 15, 'rna3p_pyr': 15} Link IDs: {'rna2p': 7, 'rna3p': 29} Chain: "I" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1363 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 170} Chain: "J" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2643 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain: "K" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 725 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 14} Link IDs: {'rna2p': 8, 'rna3p': 25} Chain breaks: 1 Chain: "L" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1972 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 235} Chain: "M" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1363 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 170} Chain: "N" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1375 Classifications: {'DNA': 67} Link IDs: {'rna3p': 66} Chain: "O" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 619 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "F" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131} Chain breaks: 3 Time building chain proxies: 5.15, per 1000 atoms: 0.23 Number of scatterers: 22777 At special positions: 0 Unit cell: (119.7, 139.08, 249.66, 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 49 16.00 P 339 15.00 O 5038 8.00 N 3996 7.00 C 13355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 918.8 milliseconds 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3734 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 18 sheets defined 60.3% alpha, 8.4% beta 101 base pairs and 205 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 22 through 40 removed outlier: 4.090A pdb=" N VAL A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.691A pdb=" N LYS A 66 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 removed outlier: 4.224A pdb=" N ILE A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.872A pdb=" N ILE A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 166 Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.915A pdb=" N LYS A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 212 removed outlier: 4.935A pdb=" N ASP A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 250 removed outlier: 3.608A pdb=" N GLU A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 303 through 326 removed outlier: 4.457A pdb=" N ASN A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 removed outlier: 4.120A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 48 through 64 removed outlier: 3.651A pdb=" N SER B 61 " --> pdb=" O LYS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.959A pdb=" N LEU B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.826A pdb=" N ASN B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 removed outlier: 4.202A pdb=" N LEU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 131 " --> pdb=" O TRP B 127 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 168 removed outlier: 3.833A pdb=" N MET B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 182 Processing helix chain 'B' and resid 188 through 202 removed outlier: 3.544A pdb=" N LEU B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 223 removed outlier: 3.712A pdb=" N LEU B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'E' and resid 13 through 20 removed outlier: 3.524A pdb=" N PHE E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 40 Proline residue: E 31 - end of helix Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.640A pdb=" N ILE E 61 " --> pdb=" O SER E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 92 through 108 removed outlier: 4.235A pdb=" N ILE E 98 " --> pdb=" O GLY E 94 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS E 105 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.545A pdb=" N ALA E 132 " --> pdb=" O ILE E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 154 through 166 removed outlier: 4.280A pdb=" N ASN E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR E 165 " --> pdb=" O GLY E 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 191 through 200 removed outlier: 4.194A pdb=" N PHE E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 212 Processing helix chain 'E' and resid 235 through 250 removed outlier: 3.723A pdb=" N LEU E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 300 removed outlier: 3.625A pdb=" N TYR E 293 " --> pdb=" O LYS E 289 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG E 298 " --> pdb=" O GLU E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 326 removed outlier: 3.800A pdb=" N ILE E 320 " --> pdb=" O TYR E 316 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP E 321 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS E 322 " --> pdb=" O LYS E 318 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 21 Processing helix chain 'I' and resid 22 through 24 No H-bonds generated for 'chain 'I' and resid 22 through 24' Processing helix chain 'I' and resid 25 through 54 removed outlier: 3.934A pdb=" N SER I 54 " --> pdb=" O THR I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 removed outlier: 7.065A pdb=" N LYS I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 90 removed outlier: 4.697A pdb=" N ASN I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 128 removed outlier: 3.646A pdb=" N ILE I 120 " --> pdb=" O SER I 116 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR I 127 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU I 128 " --> pdb=" O ILE I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 152 removed outlier: 3.770A pdb=" N GLY I 152 " --> pdb=" O ALA I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 171 removed outlier: 4.005A pdb=" N ILE I 167 " --> pdb=" O LYS I 163 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 20 Processing helix chain 'J' and resid 22 through 40 removed outlier: 4.008A pdb=" N ASP J 27 " --> pdb=" O PRO J 23 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) Proline residue: J 31 - end of helix Processing helix chain 'J' and resid 46 through 54 removed outlier: 3.756A pdb=" N VAL J 52 " --> pdb=" O SER J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 70 removed outlier: 4.336A pdb=" N LYS J 66 " --> pdb=" O SER J 63 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS J 68 " --> pdb=" O ILE J 65 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASP J 69 " --> pdb=" O LYS J 66 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS J 70 " --> pdb=" O ASN J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.095A pdb=" N LYS J 83 " --> pdb=" O GLY J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 109 removed outlier: 4.324A pdb=" N ILE J 98 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR J 108 " --> pdb=" O HIS J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 135 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 154 through 163 removed outlier: 4.256A pdb=" N VAL J 158 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE J 159 " --> pdb=" O PHE J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 178 removed outlier: 3.729A pdb=" N LYS J 174 " --> pdb=" O GLU J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 212 removed outlier: 3.538A pdb=" N LEU J 195 " --> pdb=" O SER J 191 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP J 202 " --> pdb=" O ILE J 198 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR J 203 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 250 Processing helix chain 'J' and resid 255 through 259 removed outlier: 4.141A pdb=" N LEU J 259 " --> pdb=" O THR J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 299 removed outlier: 3.617A pdb=" N THR J 292 " --> pdb=" O ASN J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 326 removed outlier: 3.959A pdb=" N TYR J 316 " --> pdb=" O GLY J 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 12 Processing helix chain 'L' and resid 36 through 38 No H-bonds generated for 'chain 'L' and resid 36 through 38' Processing helix chain 'L' and resid 48 through 64 removed outlier: 3.740A pdb=" N ASN L 54 " --> pdb=" O ARG L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 92 Processing helix chain 'L' and resid 120 through 138 removed outlier: 3.927A pdb=" N LEU L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 168 Processing helix chain 'L' and resid 171 through 181 removed outlier: 4.261A pdb=" N LYS L 177 " --> pdb=" O PRO L 173 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP L 181 " --> pdb=" O LYS L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 202 Processing helix chain 'L' and resid 231 through 245 Processing helix chain 'M' and resid 2 through 21 removed outlier: 3.758A pdb=" N ALA M 17 " --> pdb=" O LYS M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 54 removed outlier: 4.071A pdb=" N ALA M 31 " --> pdb=" O VAL M 27 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR M 41 " --> pdb=" O PHE M 37 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N CYS M 44 " --> pdb=" O TYR M 40 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER M 54 " --> pdb=" O THR M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 62 removed outlier: 7.076A pdb=" N LYS M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP M 59 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN M 61 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL M 62 " --> pdb=" O TRP M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 65 No H-bonds generated for 'chain 'M' and resid 63 through 65' Processing helix chain 'M' and resid 66 through 89 removed outlier: 4.680A pdb=" N VAL M 75 " --> pdb=" O LEU M 71 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 128 removed outlier: 4.187A pdb=" N ILE M 124 " --> pdb=" O ILE M 120 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL M 125 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP M 126 " --> pdb=" O ARG M 122 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR M 127 " --> pdb=" O GLY M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 152 removed outlier: 3.986A pdb=" N GLY M 152 " --> pdb=" O ALA M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 172 removed outlier: 3.923A pdb=" N ARG M 166 " --> pdb=" O ALA M 162 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE M 167 " --> pdb=" O LYS M 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 51 through 63 Processing helix chain 'F' and resid 156 through 168 removed outlier: 3.570A pdb=" N THR F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 182 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 216 through 223 removed outlier: 3.684A pdb=" N VAL F 223 " --> pdb=" O GLY F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 244 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 78 removed outlier: 3.657A pdb=" N PHE A 75 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 77 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG A 86 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 221 removed outlier: 3.534A pdb=" N SER A 229 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 141 " --> pdb=" O SER A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23 removed outlier: 4.054A pdb=" N ASN B 23 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 28 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 29 " --> pdb=" O LYS B 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 104 removed outlier: 6.964A pdb=" N PHE B 115 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 100 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR B 113 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL B 102 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER B 111 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE B 104 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASN B 109 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA B 110 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N MET B 146 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 112 " --> pdb=" O MET B 146 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU B 148 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE B 114 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 207 Processing sheet with id=AA7, first strand: chain 'E' and resid 217 through 219 removed outlier: 3.560A pdb=" N SER E 229 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP E 140 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 141 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER E 262 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 269 through 270 Processing sheet with id=AA9, first strand: chain 'I' and resid 141 through 142 Processing sheet with id=AB1, first strand: chain 'J' and resid 72 through 76 removed outlier: 3.913A pdb=" N SER J 90 " --> pdb=" O ARG J 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE J 88 " --> pdb=" O PHE J 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 217 through 221 removed outlier: 3.610A pdb=" N SER J 229 " --> pdb=" O TRP J 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 269 through 270 Processing sheet with id=AB4, first strand: chain 'L' and resid 18 through 21 Processing sheet with id=AB5, first strand: chain 'L' and resid 97 through 106 removed outlier: 3.680A pdb=" N ASP L 99 " --> pdb=" O PHE L 115 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU L 105 " --> pdb=" O ASN L 109 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA L 110 " --> pdb=" O LEU L 142 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA L 144 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL L 112 " --> pdb=" O ALA L 144 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET L 146 " --> pdb=" O VAL L 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 205 through 207 Processing sheet with id=AB7, first strand: chain 'M' and resid 134 through 135 Processing sheet with id=AB8, first strand: chain 'F' and resid 32 through 34 removed outlier: 6.388A pdb=" N ILE F 33 " --> pdb=" O SER F 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 170 through 171 removed outlier: 3.647A pdb=" N CYS F 170 " --> pdb=" O TYR F 213 " (cutoff:3.500A) 818 hydrogen bonds defined for protein. 2370 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 267 hydrogen bonds 498 hydrogen bond angles 0 basepair planarities 101 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4305 1.33 - 1.45: 7277 1.45 - 1.58: 11580 1.58 - 1.70: 671 1.70 - 1.82: 88 Bond restraints: 23921 Sorted by residual: bond pdb=" N9 DA C 27 " pdb=" C4 DA C 27 " ideal model delta sigma weight residual 1.374 1.406 -0.032 6.00e-03 2.78e+04 2.76e+01 bond pdb=" C3' DG N 3 " pdb=" O3' DG N 3 " ideal model delta sigma weight residual 1.435 1.496 -0.061 1.30e-02 5.92e+03 2.17e+01 bond pdb=" N9 DG C 26 " pdb=" C4 DG C 26 " ideal model delta sigma weight residual 1.375 1.410 -0.035 8.00e-03 1.56e+04 1.97e+01 bond pdb=" C4' DG N 65 " pdb=" C3' DG N 65 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.00e-02 1.00e+04 1.95e+01 bond pdb=" C3' DC N 64 " pdb=" O3' DC N 64 " ideal model delta sigma weight residual 1.435 1.378 0.057 1.30e-02 5.92e+03 1.93e+01 ... (remaining 23916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 33052 3.33 - 6.65: 636 6.65 - 9.98: 111 9.98 - 13.31: 36 13.31 - 16.64: 3 Bond angle restraints: 33838 Sorted by residual: angle pdb=" C1' U H 52 " pdb=" N1 U H 52 " pdb=" C2 U H 52 " ideal model delta sigma weight residual 117.70 130.61 -12.91 1.20e+00 6.94e-01 1.16e+02 angle pdb=" N1 U H 52 " pdb=" C2 U H 52 " pdb=" O2 U H 52 " ideal model delta sigma weight residual 122.80 129.40 -6.60 7.00e-01 2.04e+00 8.88e+01 angle pdb=" O4' DG N 29 " pdb=" C1' DG N 29 " pdb=" N9 DG N 29 " ideal model delta sigma weight residual 108.00 114.40 -6.40 7.00e-01 2.04e+00 8.35e+01 angle pdb=" O5' G K 46 " pdb=" C5' G K 46 " pdb=" C4' G K 46 " ideal model delta sigma weight residual 109.40 115.72 -6.32 8.00e-01 1.56e+00 6.25e+01 angle pdb=" O2 U H 52 " pdb=" C2 U H 52 " pdb=" N3 U H 52 " ideal model delta sigma weight residual 122.20 116.74 5.46 7.00e-01 2.04e+00 6.09e+01 ... (remaining 33833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 12573 35.90 - 71.79: 1353 71.79 - 107.69: 68 107.69 - 143.58: 1 143.58 - 179.48: 10 Dihedral angle restraints: 14005 sinusoidal: 8243 harmonic: 5762 Sorted by residual: dihedral pdb=" O4' U D 54 " pdb=" C1' U D 54 " pdb=" N1 U D 54 " pdb=" C2 U D 54 " ideal model delta sinusoidal sigma weight residual -128.00 50.84 -178.84 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U K 54 " pdb=" C1' U K 54 " pdb=" N1 U K 54 " pdb=" C2 U K 54 " ideal model delta sinusoidal sigma weight residual 232.00 54.05 177.95 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C5' A K 53 " pdb=" C4' A K 53 " pdb=" C3' A K 53 " pdb=" O3' A K 53 " ideal model delta sinusoidal sigma weight residual 147.00 99.90 47.10 1 8.00e+00 1.56e-02 4.79e+01 ... (remaining 14002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 3710 0.132 - 0.263: 194 0.263 - 0.395: 12 0.395 - 0.526: 4 0.526 - 0.658: 1 Chirality restraints: 3921 Sorted by residual: chirality pdb=" CB VAL I 125 " pdb=" CA VAL I 125 " pdb=" CG1 VAL I 125 " pdb=" CG2 VAL I 125 " both_signs ideal model delta sigma weight residual False -2.63 -1.97 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DA G 1 " pdb=" OP1 DA G 1 " pdb=" OP2 DA G 1 " pdb=" O5' DA G 1 " both_signs ideal model delta sigma weight residual True 2.34 2.79 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" P DA N 1 " pdb=" OP1 DA N 1 " pdb=" OP2 DA N 1 " pdb=" O5' DA N 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.79 -0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 3918 not shown) Planarity restraints: 3062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 27 " 0.025 2.00e-02 2.50e+03 5.14e-02 2.65e+01 pdb=" CD GLU B 27 " -0.089 2.00e-02 2.50e+03 pdb=" OE1 GLU B 27 " 0.032 2.00e-02 2.50e+03 pdb=" OE2 GLU B 27 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G K 45 " 0.048 2.00e-02 2.50e+03 2.83e-02 2.41e+01 pdb=" N9 G K 45 " -0.072 2.00e-02 2.50e+03 pdb=" C8 G K 45 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G K 45 " -0.018 2.00e-02 2.50e+03 pdb=" C5 G K 45 " 0.008 2.00e-02 2.50e+03 pdb=" C6 G K 45 " 0.012 2.00e-02 2.50e+03 pdb=" O6 G K 45 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G K 45 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G K 45 " -0.010 2.00e-02 2.50e+03 pdb=" N2 G K 45 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G K 45 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G K 45 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 64 " 0.050 2.00e-02 2.50e+03 3.25e-02 2.38e+01 pdb=" N1 DC N 64 " -0.083 2.00e-02 2.50e+03 pdb=" C2 DC N 64 " 0.007 2.00e-02 2.50e+03 pdb=" O2 DC N 64 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DC N 64 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC N 64 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC N 64 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DC N 64 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DC N 64 " 0.000 2.00e-02 2.50e+03 ... (remaining 3059 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1887 2.74 - 3.28: 21913 3.28 - 3.82: 40650 3.82 - 4.36: 47110 4.36 - 4.90: 72362 Nonbonded interactions: 183922 Sorted by model distance: nonbonded pdb=" O4 DT N 22 " pdb=" O6 DG N 32 " model vdw 2.202 2.432 nonbonded pdb=" O ASN L 139 " pdb=" ND2 ASN L 139 " model vdw 2.280 3.120 nonbonded pdb=" O5' A H 53 " pdb=" O4' A H 53 " model vdw 2.493 2.432 nonbonded pdb=" O5' DA G 27 " pdb=" O4' DA G 27 " model vdw 2.495 2.432 nonbonded pdb=" O5' DC C 4 " pdb=" O4' DC C 4 " model vdw 2.506 2.432 ... (remaining 183917 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' selection = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'B' selection = (chain 'L' and resid 3 through 245) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' } ncs_group { reference = (chain 'D' and (resid 45 through 64 or resid 69 through 81)) selection = (chain 'H' and (resid 45 through 64 or resid 69 through 81)) selection = (chain 'K' and resid 45 through 81) } ncs_group { reference = chain 'I' selection = chain 'M' } 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: 5.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.770 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.007 0.068 23921 Z= 0.487 Angle : 1.236 16.637 33838 Z= 0.830 Chirality : 0.070 0.658 3921 Planarity : 0.008 0.088 3062 Dihedral : 23.305 179.475 10271 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.80 % Allowed : 20.72 % Favored : 78.48 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.17), residues: 1933 helix: -0.94 (0.14), residues: 1068 sheet: -0.66 (0.41), residues: 172 loop : -0.88 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG J 281 TYR 0.079 0.005 TYR F 217 PHE 0.043 0.003 PHE E 60 TRP 0.046 0.003 TRP E 140 HIS 0.030 0.003 HIS I 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.49 (23921) covalent geometry : angle 1.23611 / 0.83 (33838) hydrogen bonds : bond 0.13805 / 8.92 ( 1085) hydrogen bonds : angle 5.98476 / 4.23 ( 2868) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 445 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8531 (t0) cc_final: 0.8175 (t0) REVERT: A 248 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7576 (mp0) REVERT: A 321 ASP cc_start: 0.8201 (t0) cc_final: 0.7941 (t0) REVERT: B 79 ASP cc_start: 0.8159 (m-30) cc_final: 0.7845 (m-30) REVERT: B 113 TYR cc_start: 0.7741 (m-10) cc_final: 0.7487 (m-10) REVERT: B 124 LYS cc_start: 0.8936 (pttm) cc_final: 0.8692 (pptt) REVERT: B 158 MET cc_start: 0.8246 (tpt) cc_final: 0.7633 (tpp) REVERT: B 164 MET cc_start: 0.8816 (mmm) cc_final: 0.8590 (mmm) REVERT: B 171 ASP cc_start: 0.8538 (t0) cc_final: 0.8048 (t0) REVERT: B 208 ASP cc_start: 0.7950 (t0) cc_final: 0.7555 (p0) REVERT: B 215 MET cc_start: 0.7306 (mtp) cc_final: 0.7076 (mtp) REVERT: E 201 LYS cc_start: 0.7953 (tttm) cc_final: 0.7232 (tppt) REVERT: E 251 ASN cc_start: 0.7165 (m-40) cc_final: 0.6820 (p0) REVERT: E 287 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7229 (mtm-85) REVERT: I 5 TYR cc_start: 0.8274 (t80) cc_final: 0.8027 (t80) REVERT: I 6 GLU cc_start: 0.8440 (tp30) cc_final: 0.8178 (tp30) REVERT: I 11 LEU cc_start: 0.8762 (mt) cc_final: 0.8521 (mt) REVERT: I 20 ARG cc_start: 0.8379 (mmp80) cc_final: 0.8167 (mmp80) REVERT: I 56 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7782 (tp30) REVERT: I 82 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7501 (tm-30) REVERT: I 165 LYS cc_start: 0.9176 (tppt) cc_final: 0.8866 (ttpp) REVERT: I 166 ARG cc_start: 0.8237 (ttt180) cc_final: 0.7934 (ttt180) REVERT: J 1 MET cc_start: 0.5752 (mmm) cc_final: 0.5294 (mmt) REVERT: J 31 PRO cc_start: 0.8072 (Cg_exo) cc_final: 0.7806 (Cg_endo) REVERT: J 57 SER cc_start: 0.8482 (m) cc_final: 0.7954 (p) REVERT: J 183 ASN cc_start: 0.8374 (m-40) cc_final: 0.7796 (t0) REVERT: J 237 GLU cc_start: 0.8147 (mp0) cc_final: 0.7928 (mm-30) REVERT: J 290 LEU cc_start: 0.8239 (mt) cc_final: 0.7745 (mt) REVERT: J 314 VAL cc_start: 0.7572 (t) cc_final: 0.7044 (p) REVERT: J 318 LYS cc_start: 0.8106 (mttt) cc_final: 0.7525 (mmmt) REVERT: J 321 ASP cc_start: 0.7871 (t0) cc_final: 0.7492 (t0) REVERT: L 14 TYR cc_start: 0.7019 (m-80) cc_final: 0.6747 (m-80) REVERT: L 67 VAL cc_start: 0.9057 (t) cc_final: 0.8583 (m) REVERT: L 81 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7151 (mm-30) REVERT: L 85 LYS cc_start: 0.8775 (mptt) cc_final: 0.8499 (mptt) REVERT: L 103 SER cc_start: 0.8158 (m) cc_final: 0.7682 (p) REVERT: L 124 LYS cc_start: 0.8298 (mttt) cc_final: 0.7945 (ptpp) REVERT: L 158 MET cc_start: 0.6366 (mmm) cc_final: 0.5649 (mmt) REVERT: L 229 LYS cc_start: 0.7684 (ttmt) cc_final: 0.7315 (ttmm) REVERT: F 32 ASP cc_start: 0.7634 (m-30) cc_final: 0.6958 (t0) REVERT: F 57 LYS cc_start: 0.8807 (tppt) cc_final: 0.8501 (tppt) REVERT: F 202 LYS cc_start: 0.9375 (mmtm) cc_final: 0.9016 (mmtt) outliers start: 14 outliers final: 3 residues processed: 448 average time/residue: 0.1695 time to fit residues: 114.8739 Evaluate side-chains 438 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 435 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain F residue 222 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN A 241 GLN A 295 HIS B 23 ASN B 109 ASN ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 241 GLN I 14 GLN J 164 ASN M 136 ASN M 169 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.146024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.122758 restraints weight = 61628.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.126198 restraints weight = 33391.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.127577 restraints weight = 18691.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.128248 restraints weight = 15143.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.128381 restraints weight = 14189.041| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 23921 Z= 0.205 Angle : 0.753 10.968 33838 Z= 0.423 Chirality : 0.048 0.405 3921 Planarity : 0.005 0.054 3062 Dihedral : 26.263 179.091 6294 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.08 % Allowed : 17.41 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.66 (0.18), residues: 1933 helix: -0.02 (0.15), residues: 1080 sheet: -0.80 (0.40), residues: 187 loop : -0.81 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 298 TYR 0.023 0.002 TYR I 127 PHE 0.028 0.002 PHE E 227 TRP 0.021 0.002 TRP E 140 HIS 0.007 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 (23921) covalent geometry : angle 0.75287 / 0.42 (33838) hydrogen bonds : bond 0.06114 / 4.18 ( 1085) hydrogen bonds : angle 4.82348 / 3.40 ( 2868) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 434 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8571 (t0) cc_final: 0.8225 (t0) REVERT: A 205 ASP cc_start: 0.8396 (t0) cc_final: 0.8151 (t0) REVERT: A 321 ASP cc_start: 0.8196 (t0) cc_final: 0.7952 (t0) REVERT: B 14 TYR cc_start: 0.8703 (m-80) cc_final: 0.8476 (m-80) REVERT: B 16 ILE cc_start: 0.9107 (pt) cc_final: 0.8704 (tp) REVERT: B 20 ARG cc_start: 0.8923 (mmm-85) cc_final: 0.8649 (ttt-90) REVERT: B 79 ASP cc_start: 0.8019 (m-30) cc_final: 0.7643 (m-30) REVERT: B 124 LYS cc_start: 0.8968 (pttm) cc_final: 0.8181 (pttm) REVERT: B 164 MET cc_start: 0.8793 (mmm) cc_final: 0.8195 (mmm) REVERT: B 180 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7638 (mp0) REVERT: B 208 ASP cc_start: 0.7898 (t0) cc_final: 0.7314 (p0) REVERT: B 209 ARG cc_start: 0.5196 (mmp-170) cc_final: 0.4871 (mmt180) REVERT: B 215 MET cc_start: 0.7691 (mtp) cc_final: 0.7426 (mtp) REVERT: E 201 LYS cc_start: 0.8057 (tttm) cc_final: 0.7544 (tppt) REVERT: E 251 ASN cc_start: 0.7215 (m-40) cc_final: 0.6899 (p0) REVERT: I 6 GLU cc_start: 0.8566 (tp30) cc_final: 0.8259 (tp30) REVERT: I 11 LEU cc_start: 0.8865 (mt) cc_final: 0.8600 (mt) REVERT: I 109 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: J 1 MET cc_start: 0.5791 (mmm) cc_final: 0.5323 (mmt) REVERT: J 31 PRO cc_start: 0.8101 (Cg_exo) cc_final: 0.7846 (Cg_endo) REVERT: J 57 SER cc_start: 0.8463 (m) cc_final: 0.8022 (p) REVERT: J 109 ASN cc_start: 0.8529 (t0) cc_final: 0.8267 (t0) REVERT: J 183 ASN cc_start: 0.8308 (m-40) cc_final: 0.7774 (t0) REVERT: J 291 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7498 (mtt-85) REVERT: J 314 VAL cc_start: 0.7715 (t) cc_final: 0.7291 (p) REVERT: J 318 LYS cc_start: 0.8243 (mttt) cc_final: 0.7738 (mmmt) REVERT: J 321 ASP cc_start: 0.7877 (t0) cc_final: 0.7478 (t0) REVERT: L 67 VAL cc_start: 0.9084 (t) cc_final: 0.8656 (m) REVERT: L 81 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7221 (mm-30) REVERT: L 158 MET cc_start: 0.5805 (mmm) cc_final: 0.5258 (mmt) REVERT: L 229 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7361 (ttmm) REVERT: M 40 TYR cc_start: 0.7891 (m-80) cc_final: 0.7557 (m-10) REVERT: F 9 TYR cc_start: 0.5203 (t80) cc_final: 0.4567 (t80) REVERT: F 32 ASP cc_start: 0.7644 (m-30) cc_final: 0.6813 (t0) REVERT: F 191 TRP cc_start: 0.8682 (t60) cc_final: 0.8226 (t60) REVERT: F 213 TYR cc_start: 0.6488 (m-80) cc_final: 0.6263 (m-80) outliers start: 54 outliers final: 31 residues processed: 456 average time/residue: 0.1660 time to fit residues: 114.9394 Evaluate side-chains 450 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 418 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 69 ASN Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 239 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [132, 196, 164, 138, 66, 45, 106, 55, 85, 72, 210] chunk 132 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 210 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 HIS E 59 HIS E 241 GLN ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 ASN M 169 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.144991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.121558 restraints weight = 62011.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.124922 restraints weight = 33731.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.126148 restraints weight = 19343.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.126932 restraints weight = 15696.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.127078 restraints weight = 14159.951| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23921 Z= 0.203 Angle : 0.727 11.065 33838 Z= 0.409 Chirality : 0.047 0.374 3921 Planarity : 0.005 0.106 3062 Dihedral : 26.254 178.802 6290 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.31 % Allowed : 18.61 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.51 (0.19), residues: 1933 helix: 0.20 (0.15), residues: 1075 sheet: -0.91 (0.40), residues: 184 loop : -0.85 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 35 TYR 0.026 0.002 TYR J 71 PHE 0.023 0.002 PHE E 227 TRP 0.013 0.001 TRP E 140 HIS 0.010 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (23921) covalent geometry : angle 0.72729 / 0.41 (33838) hydrogen bonds : bond 0.05962 / 4.06 ( 1085) hydrogen bonds : angle 4.60443 / 3.25 ( 2868) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 432 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: A 111 ASN cc_start: 0.8581 (t0) cc_final: 0.8245 (t0) REVERT: A 321 ASP cc_start: 0.8217 (t70) cc_final: 0.7993 (t0) REVERT: B 16 ILE cc_start: 0.9085 (pt) cc_final: 0.8685 (tp) REVERT: B 79 ASP cc_start: 0.7943 (m-30) cc_final: 0.7559 (m-30) REVERT: B 119 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6815 (tpt) REVERT: B 124 LYS cc_start: 0.8967 (pttm) cc_final: 0.8669 (pttm) REVERT: B 164 MET cc_start: 0.8803 (mmm) cc_final: 0.8592 (mmm) REVERT: B 192 LEU cc_start: 0.8786 (tp) cc_final: 0.8514 (mp) REVERT: B 208 ASP cc_start: 0.7924 (t0) cc_final: 0.7383 (p0) REVERT: B 209 ARG cc_start: 0.5391 (mmp-170) cc_final: 0.4979 (mmt180) REVERT: B 235 ASP cc_start: 0.7947 (m-30) cc_final: 0.7663 (m-30) REVERT: E 128 ILE cc_start: 0.8173 (pt) cc_final: 0.7935 (pt) REVERT: E 201 LYS cc_start: 0.8022 (tttm) cc_final: 0.7570 (tppt) REVERT: E 251 ASN cc_start: 0.7213 (m-40) cc_final: 0.6846 (p0) REVERT: E 326 GLU cc_start: 0.6630 (mm-30) cc_final: 0.6193 (mp0) REVERT: I 5 TYR cc_start: 0.8320 (t80) cc_final: 0.8060 (t80) REVERT: I 6 GLU cc_start: 0.8628 (tp30) cc_final: 0.8207 (tp30) REVERT: I 11 LEU cc_start: 0.8891 (mt) cc_final: 0.8689 (mt) REVERT: I 56 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7691 (tp30) REVERT: I 82 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7907 (tm-30) REVERT: I 101 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8004 (ttmm) REVERT: I 111 MET cc_start: 0.7838 (mmp) cc_final: 0.7551 (mmp) REVERT: I 149 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8419 (tm-30) REVERT: I 153 TRP cc_start: 0.8520 (m-10) cc_final: 0.7681 (m-10) REVERT: I 165 LYS cc_start: 0.9095 (tppt) cc_final: 0.8858 (ttpp) REVERT: J 31 PRO cc_start: 0.8075 (Cg_exo) cc_final: 0.7830 (Cg_endo) REVERT: J 57 SER cc_start: 0.8506 (m) cc_final: 0.8024 (p) REVERT: J 183 ASN cc_start: 0.8368 (m-40) cc_final: 0.7769 (t0) REVERT: J 314 VAL cc_start: 0.7701 (t) cc_final: 0.7332 (p) REVERT: J 318 LYS cc_start: 0.8256 (mttt) cc_final: 0.7779 (mmmt) REVERT: J 321 ASP cc_start: 0.7981 (t0) cc_final: 0.7602 (t0) REVERT: L 67 VAL cc_start: 0.9059 (t) cc_final: 0.8634 (m) REVERT: L 81 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7283 (mm-30) REVERT: L 158 MET cc_start: 0.5717 (mmm) cc_final: 0.5113 (mmt) REVERT: L 229 LYS cc_start: 0.7714 (ttmt) cc_final: 0.7400 (ttmm) REVERT: M 40 TYR cc_start: 0.7909 (m-80) cc_final: 0.7677 (m-10) REVERT: F 191 TRP cc_start: 0.8740 (t60) cc_final: 0.8305 (t60) REVERT: F 201 LYS cc_start: 0.8920 (mmtt) cc_final: 0.7341 (mmtt) REVERT: F 205 ILE cc_start: 0.8914 (mt) cc_final: 0.8683 (mp) REVERT: F 213 TYR cc_start: 0.6504 (m-80) cc_final: 0.6266 (m-80) outliers start: 58 outliers final: 39 residues processed: 457 average time/residue: 0.1619 time to fit residues: 111.9520 Evaluate side-chains 468 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 426 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 218 TYR Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 69 ASN Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 239 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [165, 36, 144, 42, 10, 106, 198, 167, 179, 3, 0] chunk 165 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 198 optimal weight: 0.0470 chunk 167 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 HIS B 109 ASN E 59 HIS ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.145726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.122280 restraints weight = 62276.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.125746 restraints weight = 34556.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.127416 restraints weight = 19425.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.127739 restraints weight = 15127.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.127903 restraints weight = 14089.758| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23921 Z= 0.169 Angle : 0.697 10.591 33838 Z= 0.389 Chirality : 0.045 0.382 3921 Planarity : 0.004 0.064 3062 Dihedral : 26.275 179.227 6288 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.54 % Allowed : 19.69 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.32 (0.19), residues: 1933 helix: 0.44 (0.16), residues: 1075 sheet: -0.94 (0.40), residues: 182 loop : -0.90 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 200 TYR 0.033 0.002 TYR F 217 PHE 0.019 0.002 PHE E 227 TRP 0.010 0.001 TRP J 101 HIS 0.010 0.001 HIS I 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (23921) covalent geometry : angle 0.69717 / 0.39 (33838) hydrogen bonds : bond 0.05473 / 3.73 ( 1085) hydrogen bonds : angle 4.43563 / 3.13 ( 2868) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 442 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: A 111 ASN cc_start: 0.8522 (t0) cc_final: 0.8208 (t0) REVERT: A 205 ASP cc_start: 0.8407 (t0) cc_final: 0.8160 (t0) REVERT: A 309 ARG cc_start: 0.8280 (ptm-80) cc_final: 0.7994 (ptm-80) REVERT: A 321 ASP cc_start: 0.8205 (t70) cc_final: 0.7974 (t0) REVERT: B 14 TYR cc_start: 0.8698 (m-80) cc_final: 0.8479 (m-10) REVERT: B 16 ILE cc_start: 0.9110 (pt) cc_final: 0.8667 (tp) REVERT: B 79 ASP cc_start: 0.7994 (m-30) cc_final: 0.7604 (m-30) REVERT: B 124 LYS cc_start: 0.8884 (pttm) cc_final: 0.8623 (pttm) REVERT: B 208 ASP cc_start: 0.7891 (t0) cc_final: 0.7431 (p0) REVERT: B 209 ARG cc_start: 0.5484 (mmp-170) cc_final: 0.5139 (mmt180) REVERT: B 235 ASP cc_start: 0.7929 (m-30) cc_final: 0.7568 (m-30) REVERT: E 92 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.4741 (ttt-90) REVERT: E 128 ILE cc_start: 0.8172 (pt) cc_final: 0.7939 (pt) REVERT: E 147 ARG cc_start: 0.6942 (tpp-160) cc_final: 0.6613 (tpp-160) REVERT: E 181 TYR cc_start: 0.7349 (t80) cc_final: 0.7010 (t80) REVERT: E 201 LYS cc_start: 0.8025 (tttm) cc_final: 0.7591 (tppt) REVERT: E 251 ASN cc_start: 0.7131 (m-40) cc_final: 0.6762 (p0) REVERT: E 267 ARG cc_start: 0.7170 (ttm110) cc_final: 0.6931 (ttm110) REVERT: I 5 TYR cc_start: 0.8418 (t80) cc_final: 0.8068 (t80) REVERT: I 6 GLU cc_start: 0.8623 (tp30) cc_final: 0.8229 (tp30) REVERT: I 11 LEU cc_start: 0.8904 (mt) cc_final: 0.8620 (mt) REVERT: I 82 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7890 (tm-30) REVERT: I 109 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: I 149 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8359 (tm-30) REVERT: I 153 TRP cc_start: 0.8510 (m-10) cc_final: 0.7557 (m-10) REVERT: I 165 LYS cc_start: 0.9119 (tppt) cc_final: 0.8912 (ttpp) REVERT: I 170 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7163 (mt-10) REVERT: J 31 PRO cc_start: 0.8149 (Cg_exo) cc_final: 0.7894 (Cg_endo) REVERT: J 39 ARG cc_start: 0.7964 (tpp80) cc_final: 0.7416 (tpt-90) REVERT: J 57 SER cc_start: 0.8520 (m) cc_final: 0.8073 (p) REVERT: J 147 ARG cc_start: 0.6184 (OUTLIER) cc_final: 0.5978 (mtm110) REVERT: J 183 ASN cc_start: 0.8351 (m-40) cc_final: 0.7749 (t0) REVERT: J 314 VAL cc_start: 0.7678 (t) cc_final: 0.7329 (p) REVERT: J 318 LYS cc_start: 0.8238 (mttt) cc_final: 0.7810 (mmmt) REVERT: J 321 ASP cc_start: 0.7949 (t0) cc_final: 0.7566 (t0) REVERT: L 67 VAL cc_start: 0.9036 (t) cc_final: 0.8608 (m) REVERT: L 81 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7245 (mm-30) REVERT: L 151 ASN cc_start: 0.8138 (t0) cc_final: 0.7933 (t0) REVERT: L 229 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7330 (ttmm) REVERT: F 191 TRP cc_start: 0.8699 (t60) cc_final: 0.8279 (t60) REVERT: F 200 ARG cc_start: 0.7439 (ppt170) cc_final: 0.6861 (ppt170) REVERT: F 201 LYS cc_start: 0.8699 (mttt) cc_final: 0.7505 (mmtt) REVERT: F 213 TYR cc_start: 0.6497 (m-80) cc_final: 0.6234 (m-80) outliers start: 62 outliers final: 48 residues processed: 476 average time/residue: 0.1656 time to fit residues: 119.3770 Evaluate side-chains 484 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 432 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 147 ARG Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 218 TYR Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 324 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 69 ASN Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 239 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [145, 88, 210, 54, 22, 200, 62, 1, 184, 4, 187] chunk 145 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 chunk 210 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 HIS B 109 ASN E 59 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN J 208 ASN ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.145241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.121848 restraints weight = 61735.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.125411 restraints weight = 34085.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.126837 restraints weight = 19025.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.127266 restraints weight = 15197.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.127452 restraints weight = 14107.768| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23921 Z= 0.180 Angle : 0.699 11.116 33838 Z= 0.389 Chirality : 0.045 0.358 3921 Planarity : 0.005 0.065 3062 Dihedral : 26.265 179.542 6288 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.28 % Allowed : 20.66 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 1933 helix: 0.51 (0.16), residues: 1075 sheet: -1.03 (0.40), residues: 186 loop : -0.92 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 92 TYR 0.033 0.002 TYR F 217 PHE 0.018 0.002 PHE E 227 TRP 0.019 0.001 TRP E 47 HIS 0.016 0.002 HIS L 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (23921) covalent geometry : angle 0.69889 / 0.39 (33838) hydrogen bonds : bond 0.05465 / 3.71 ( 1085) hydrogen bonds : angle 4.39973 / 3.11 ( 2868) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 429 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: A 111 ASN cc_start: 0.8505 (t0) cc_final: 0.8197 (t0) REVERT: A 309 ARG cc_start: 0.8285 (ptm-80) cc_final: 0.7653 (ptm-80) REVERT: A 321 ASP cc_start: 0.8197 (t70) cc_final: 0.7950 (t0) REVERT: B 13 LYS cc_start: 0.8876 (ptmt) cc_final: 0.8614 (ptmt) REVERT: B 14 TYR cc_start: 0.8670 (m-80) cc_final: 0.8446 (m-10) REVERT: B 16 ILE cc_start: 0.9095 (pt) cc_final: 0.8622 (tp) REVERT: B 20 ARG cc_start: 0.8910 (mmm-85) cc_final: 0.8647 (ttt-90) REVERT: B 79 ASP cc_start: 0.8040 (m-30) cc_final: 0.7637 (m-30) REVERT: B 124 LYS cc_start: 0.8870 (pttm) cc_final: 0.8553 (pttp) REVERT: B 164 MET cc_start: 0.8929 (mmm) cc_final: 0.8386 (mmm) REVERT: B 192 LEU cc_start: 0.8762 (tp) cc_final: 0.8536 (mp) REVERT: B 208 ASP cc_start: 0.7869 (t0) cc_final: 0.7417 (p0) REVERT: B 209 ARG cc_start: 0.5570 (mmp-170) cc_final: 0.5065 (mmt180) REVERT: B 235 ASP cc_start: 0.7938 (m-30) cc_final: 0.7543 (m-30) REVERT: E 92 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.4747 (ttt-90) REVERT: E 147 ARG cc_start: 0.6884 (tpp-160) cc_final: 0.6590 (tpp-160) REVERT: E 201 LYS cc_start: 0.8038 (tttm) cc_final: 0.7633 (tppt) REVERT: E 251 ASN cc_start: 0.7050 (m-40) cc_final: 0.6711 (p0) REVERT: I 5 TYR cc_start: 0.8429 (t80) cc_final: 0.8093 (t80) REVERT: I 6 GLU cc_start: 0.8588 (tp30) cc_final: 0.8180 (tp30) REVERT: I 109 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7730 (tp30) REVERT: I 149 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8352 (tm-30) REVERT: I 153 TRP cc_start: 0.8528 (m-10) cc_final: 0.7763 (m-10) REVERT: I 170 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7201 (mt-10) REVERT: J 31 PRO cc_start: 0.8179 (Cg_exo) cc_final: 0.7935 (Cg_endo) REVERT: J 57 SER cc_start: 0.8521 (m) cc_final: 0.8114 (p) REVERT: J 187 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7367 (tp-100) REVERT: J 314 VAL cc_start: 0.7741 (t) cc_final: 0.7419 (p) REVERT: J 318 LYS cc_start: 0.8230 (mttt) cc_final: 0.7842 (mmmt) REVERT: J 321 ASP cc_start: 0.7952 (t0) cc_final: 0.7566 (t0) REVERT: L 67 VAL cc_start: 0.8981 (t) cc_final: 0.8590 (m) REVERT: L 81 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7255 (mm-30) REVERT: L 151 ASN cc_start: 0.8119 (t0) cc_final: 0.7877 (t0) REVERT: L 158 MET cc_start: 0.5884 (mmm) cc_final: 0.5128 (mmt) REVERT: L 229 LYS cc_start: 0.7670 (ttmt) cc_final: 0.7343 (ttmm) REVERT: F 168 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.7103 (p90) REVERT: F 190 ASP cc_start: 0.8988 (p0) cc_final: 0.8497 (p0) REVERT: F 191 TRP cc_start: 0.8661 (t60) cc_final: 0.8252 (t60) REVERT: F 194 LYS cc_start: 0.7952 (mttt) cc_final: 0.7323 (mmtt) REVERT: F 200 ARG cc_start: 0.7554 (ppt170) cc_final: 0.6947 (ppt170) REVERT: F 201 LYS cc_start: 0.8646 (mttt) cc_final: 0.7353 (mttt) REVERT: F 213 TYR cc_start: 0.6379 (m-80) cc_final: 0.6087 (m-80) outliers start: 75 outliers final: 57 residues processed: 469 average time/residue: 0.1625 time to fit residues: 115.5249 Evaluate side-chains 483 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 421 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 187 GLN Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain J residue 218 TYR Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 324 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 69 ASN Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 239 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [9, 8, 103, 197, 39, 117, 42, 140, 137, 167, 68] chunk 9 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 HIS B 109 ASN E 59 HIS J 208 ASN ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.145538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.122176 restraints weight = 62166.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.125806 restraints weight = 35023.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.126785 restraints weight = 20046.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.127608 restraints weight = 15902.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.127783 restraints weight = 14133.499| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23921 Z= 0.168 Angle : 0.695 12.241 33838 Z= 0.385 Chirality : 0.044 0.352 3921 Planarity : 0.005 0.065 3062 Dihedral : 26.252 179.395 6288 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.39 % Allowed : 21.58 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.22 (0.19), residues: 1933 helix: 0.57 (0.16), residues: 1076 sheet: -0.95 (0.40), residues: 184 loop : -0.93 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 20 TYR 0.037 0.002 TYR F 217 PHE 0.018 0.002 PHE E 227 TRP 0.015 0.001 TRP E 47 HIS 0.009 0.001 HIS L 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (23921) covalent geometry : angle 0.69534 / 0.39 (33838) hydrogen bonds : bond 0.05316 / 3.62 ( 1085) hydrogen bonds : angle 4.36704 / 3.09 ( 2868) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 435 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: A 111 ASN cc_start: 0.8526 (t0) cc_final: 0.8204 (t0) REVERT: A 205 ASP cc_start: 0.8398 (t0) cc_final: 0.8190 (t0) REVERT: A 309 ARG cc_start: 0.8296 (ptm-80) cc_final: 0.7955 (ptm-80) REVERT: A 321 ASP cc_start: 0.8225 (t70) cc_final: 0.7987 (t0) REVERT: B 13 LYS cc_start: 0.8883 (ptmt) cc_final: 0.8504 (ptmt) REVERT: B 14 TYR cc_start: 0.8672 (m-80) cc_final: 0.8422 (m-10) REVERT: B 16 ILE cc_start: 0.9096 (pt) cc_final: 0.8626 (tp) REVERT: B 20 ARG cc_start: 0.8887 (mmm-85) cc_final: 0.8652 (ttt-90) REVERT: B 79 ASP cc_start: 0.8032 (m-30) cc_final: 0.7629 (m-30) REVERT: B 124 LYS cc_start: 0.8859 (pttm) cc_final: 0.8454 (pttm) REVERT: B 164 MET cc_start: 0.8916 (mmm) cc_final: 0.8500 (mmm) REVERT: B 208 ASP cc_start: 0.7857 (t0) cc_final: 0.7392 (p0) REVERT: B 209 ARG cc_start: 0.5514 (mmp-170) cc_final: 0.5016 (mmt180) REVERT: B 235 ASP cc_start: 0.7926 (m-30) cc_final: 0.7521 (m-30) REVERT: E 92 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.4737 (ttt-90) REVERT: E 147 ARG cc_start: 0.6791 (tpp-160) cc_final: 0.6468 (tpp-160) REVERT: E 153 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7946 (tp) REVERT: E 201 LYS cc_start: 0.8006 (tttm) cc_final: 0.7595 (tppt) REVERT: E 251 ASN cc_start: 0.7075 (m-40) cc_final: 0.6714 (p0) REVERT: I 5 TYR cc_start: 0.8418 (t80) cc_final: 0.8079 (t80) REVERT: I 6 GLU cc_start: 0.8626 (tp30) cc_final: 0.8171 (tp30) REVERT: I 20 ARG cc_start: 0.8672 (mmp80) cc_final: 0.7734 (mmp80) REVERT: I 109 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: I 149 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8604 (tm-30) REVERT: J 31 PRO cc_start: 0.8195 (Cg_exo) cc_final: 0.7940 (Cg_endo) REVERT: J 57 SER cc_start: 0.8510 (m) cc_final: 0.8103 (p) REVERT: J 314 VAL cc_start: 0.7712 (t) cc_final: 0.7400 (p) REVERT: J 318 LYS cc_start: 0.8244 (mttt) cc_final: 0.7835 (mmmt) REVERT: J 321 ASP cc_start: 0.7974 (t0) cc_final: 0.7557 (t0) REVERT: L 14 TYR cc_start: 0.6719 (m-80) cc_final: 0.6330 (m-80) REVERT: L 67 VAL cc_start: 0.8980 (t) cc_final: 0.8598 (m) REVERT: L 81 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7255 (mm-30) REVERT: L 151 ASN cc_start: 0.8179 (t0) cc_final: 0.7963 (t0) REVERT: L 158 MET cc_start: 0.5845 (mmm) cc_final: 0.5109 (mmt) REVERT: L 229 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7383 (ttmm) REVERT: F 164 MET cc_start: 0.8298 (tpt) cc_final: 0.7755 (tpt) REVERT: F 168 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6832 (p90) REVERT: F 190 ASP cc_start: 0.9025 (p0) cc_final: 0.8481 (p0) REVERT: F 191 TRP cc_start: 0.8690 (t60) cc_final: 0.8302 (t60) REVERT: F 194 LYS cc_start: 0.7923 (mttt) cc_final: 0.7312 (mmtt) REVERT: F 200 ARG cc_start: 0.7609 (ppt170) cc_final: 0.6961 (ppt170) REVERT: F 201 LYS cc_start: 0.8647 (mttt) cc_final: 0.7340 (mmtt) REVERT: F 213 TYR cc_start: 0.6340 (m-80) cc_final: 0.5947 (m-80) outliers start: 77 outliers final: 55 residues processed: 474 average time/residue: 0.1597 time to fit residues: 114.7668 Evaluate side-chains 487 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 427 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain J residue 218 TYR Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 324 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 69 ASN Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 239 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [210, 106, 207, 65, 205, 123, 30, 124, 208, 186, 39] chunk 210 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 124 optimal weight: 0.0980 chunk 208 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 HIS B 109 ASN E 59 HIS ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN J 208 ASN ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.145312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.121909 restraints weight = 61705.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.125350 restraints weight = 34554.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.126375 restraints weight = 19749.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.127270 restraints weight = 16329.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.127395 restraints weight = 14616.225| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23921 Z= 0.179 Angle : 0.708 12.914 33838 Z= 0.390 Chirality : 0.044 0.355 3921 Planarity : 0.005 0.064 3062 Dihedral : 26.245 179.212 6288 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.85 % Allowed : 21.75 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.23 (0.19), residues: 1933 helix: 0.57 (0.16), residues: 1080 sheet: -0.96 (0.40), residues: 186 loop : -0.96 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 20 TYR 0.030 0.002 TYR E 181 PHE 0.017 0.002 PHE E 227 TRP 0.015 0.001 TRP E 47 HIS 0.010 0.001 HIS L 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (23921) covalent geometry : angle 0.70847 / 0.39 (33838) hydrogen bonds : bond 0.05383 / 3.65 ( 1085) hydrogen bonds : angle 4.36605 / 3.09 ( 2868) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 431 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: A 111 ASN cc_start: 0.8525 (t0) cc_final: 0.8221 (t0) REVERT: A 309 ARG cc_start: 0.8293 (ptm-80) cc_final: 0.7970 (ptm-80) REVERT: A 321 ASP cc_start: 0.8226 (t70) cc_final: 0.7994 (t0) REVERT: B 13 LYS cc_start: 0.8897 (ptmt) cc_final: 0.8368 (pttm) REVERT: B 14 TYR cc_start: 0.8660 (m-80) cc_final: 0.8423 (m-10) REVERT: B 16 ILE cc_start: 0.9100 (pt) cc_final: 0.8638 (tp) REVERT: B 20 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8638 (ttt-90) REVERT: B 79 ASP cc_start: 0.8032 (m-30) cc_final: 0.7634 (m-30) REVERT: B 81 GLU cc_start: 0.7619 (pt0) cc_final: 0.6625 (pp20) REVERT: B 124 LYS cc_start: 0.8880 (pttm) cc_final: 0.8527 (pttm) REVERT: B 164 MET cc_start: 0.8903 (mmm) cc_final: 0.8494 (mmm) REVERT: B 208 ASP cc_start: 0.7829 (t0) cc_final: 0.7387 (p0) REVERT: B 209 ARG cc_start: 0.5580 (mmp-170) cc_final: 0.5099 (mmt180) REVERT: B 235 ASP cc_start: 0.7925 (m-30) cc_final: 0.7455 (m-30) REVERT: E 92 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.4784 (ttt-90) REVERT: E 153 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7930 (tp) REVERT: E 201 LYS cc_start: 0.8033 (tttm) cc_final: 0.7622 (tppt) REVERT: E 251 ASN cc_start: 0.7076 (m-40) cc_final: 0.6725 (p0) REVERT: I 5 TYR cc_start: 0.8353 (t80) cc_final: 0.8065 (t80) REVERT: I 6 GLU cc_start: 0.8582 (tp30) cc_final: 0.8144 (tp30) REVERT: I 9 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7975 (tm-30) REVERT: I 56 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: I 87 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7250 (tm-30) REVERT: I 107 SER cc_start: 0.8179 (m) cc_final: 0.7918 (t) REVERT: I 109 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7851 (tp30) REVERT: I 149 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8700 (tm-30) REVERT: I 170 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7187 (mt-10) REVERT: J 31 PRO cc_start: 0.8228 (Cg_exo) cc_final: 0.7981 (Cg_endo) REVERT: J 57 SER cc_start: 0.8523 (m) cc_final: 0.8119 (p) REVERT: J 187 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7385 (tp-100) REVERT: J 302 ILE cc_start: 0.7075 (mm) cc_final: 0.6658 (tp) REVERT: J 314 VAL cc_start: 0.7744 (t) cc_final: 0.7447 (p) REVERT: J 318 LYS cc_start: 0.8253 (mttt) cc_final: 0.7912 (mmmt) REVERT: J 321 ASP cc_start: 0.7961 (t0) cc_final: 0.7501 (t0) REVERT: L 67 VAL cc_start: 0.8974 (t) cc_final: 0.8590 (m) REVERT: L 81 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7252 (mm-30) REVERT: L 103 SER cc_start: 0.7925 (m) cc_final: 0.7532 (p) REVERT: L 151 ASN cc_start: 0.8146 (t0) cc_final: 0.7919 (t0) REVERT: L 158 MET cc_start: 0.5838 (mmm) cc_final: 0.5106 (mmt) REVERT: L 229 LYS cc_start: 0.7677 (ttmt) cc_final: 0.7388 (ttmm) REVERT: F 164 MET cc_start: 0.8327 (tpt) cc_final: 0.7832 (tpt) REVERT: F 168 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6890 (p90) REVERT: F 190 ASP cc_start: 0.8998 (p0) cc_final: 0.8490 (p0) REVERT: F 191 TRP cc_start: 0.8636 (t60) cc_final: 0.8257 (t60) REVERT: F 194 LYS cc_start: 0.7894 (mttt) cc_final: 0.7281 (mmtt) REVERT: F 200 ARG cc_start: 0.7570 (ppt170) cc_final: 0.6653 (ppt170) REVERT: F 201 LYS cc_start: 0.8675 (mttt) cc_final: 0.7501 (mmtt) REVERT: F 213 TYR cc_start: 0.6305 (m-80) cc_final: 0.5954 (m-80) REVERT: F 217 TYR cc_start: 0.7520 (p90) cc_final: 0.7248 (p90) outliers start: 85 outliers final: 61 residues processed: 479 average time/residue: 0.1567 time to fit residues: 114.2402 Evaluate side-chains 488 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 420 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 187 GLN Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 218 TYR Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 324 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 69 ASN Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 239 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [146, 5, 128, 219, 103, 172, 51, 74, 180, 35, 162] chunk 146 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 162 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN A 295 HIS B 109 ASN E 59 HIS ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN M 169 GLN F 193 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.145856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.122531 restraints weight = 61558.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.126240 restraints weight = 33801.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.127517 restraints weight = 18630.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.127876 restraints weight = 15409.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.128449 restraints weight = 14007.439| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23921 Z= 0.163 Angle : 0.710 12.142 33838 Z= 0.387 Chirality : 0.044 0.356 3921 Planarity : 0.005 0.068 3062 Dihedral : 26.230 179.273 6288 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.05 % Allowed : 22.95 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.16 (0.19), residues: 1933 helix: 0.61 (0.16), residues: 1080 sheet: -0.96 (0.39), residues: 195 loop : -0.88 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 267 TYR 0.029 0.002 TYR J 71 PHE 0.018 0.001 PHE E 227 TRP 0.018 0.001 TRP I 153 HIS 0.013 0.001 HIS L 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (23921) covalent geometry : angle 0.70989 / 0.39 (33838) hydrogen bonds : bond 0.05165 / 3.51 ( 1085) hydrogen bonds : angle 4.33436 / 3.06 ( 2868) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 433 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: A 111 ASN cc_start: 0.8484 (t0) cc_final: 0.8189 (t0) REVERT: A 205 ASP cc_start: 0.8377 (t0) cc_final: 0.8169 (t0) REVERT: A 309 ARG cc_start: 0.8237 (ptm-80) cc_final: 0.7952 (ptm-80) REVERT: A 321 ASP cc_start: 0.8219 (t70) cc_final: 0.7989 (t0) REVERT: B 9 TYR cc_start: 0.8583 (t80) cc_final: 0.8381 (t80) REVERT: B 16 ILE cc_start: 0.9095 (pt) cc_final: 0.8631 (tp) REVERT: B 20 ARG cc_start: 0.8815 (mmm-85) cc_final: 0.8596 (ttt-90) REVERT: B 79 ASP cc_start: 0.8027 (m-30) cc_final: 0.7630 (m-30) REVERT: B 81 GLU cc_start: 0.7570 (pt0) cc_final: 0.6620 (pp20) REVERT: B 103 SER cc_start: 0.9124 (m) cc_final: 0.8684 (p) REVERT: B 124 LYS cc_start: 0.8875 (pttm) cc_final: 0.8471 (pttm) REVERT: B 164 MET cc_start: 0.8904 (mmm) cc_final: 0.8484 (mmm) REVERT: B 208 ASP cc_start: 0.7838 (t0) cc_final: 0.7412 (p0) REVERT: B 209 ARG cc_start: 0.5564 (mmp-170) cc_final: 0.5089 (mmt180) REVERT: B 235 ASP cc_start: 0.7902 (m-30) cc_final: 0.7442 (m-30) REVERT: E 92 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.4747 (ttt-90) REVERT: E 147 ARG cc_start: 0.6938 (tpt90) cc_final: 0.6706 (tpp-160) REVERT: E 153 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7929 (tp) REVERT: E 201 LYS cc_start: 0.7976 (tttm) cc_final: 0.7608 (tppt) REVERT: E 251 ASN cc_start: 0.6980 (m-40) cc_final: 0.6682 (p0) REVERT: E 259 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8063 (tp) REVERT: E 287 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7208 (ttm-80) REVERT: I 5 TYR cc_start: 0.8275 (t80) cc_final: 0.8043 (t80) REVERT: I 6 GLU cc_start: 0.8557 (tp30) cc_final: 0.8094 (tp30) REVERT: I 9 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7977 (tm-30) REVERT: I 20 ARG cc_start: 0.8642 (mmp80) cc_final: 0.7787 (mmp80) REVERT: I 56 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: I 107 SER cc_start: 0.8029 (m) cc_final: 0.7743 (t) REVERT: I 109 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7869 (tp30) REVERT: I 149 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8774 (tm-30) REVERT: J 1 MET cc_start: 0.5717 (mmm) cc_final: 0.5399 (mmt) REVERT: J 31 PRO cc_start: 0.8210 (Cg_exo) cc_final: 0.7964 (Cg_endo) REVERT: J 57 SER cc_start: 0.8547 (m) cc_final: 0.8143 (p) REVERT: J 187 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7465 (tp-100) REVERT: J 242 ASN cc_start: 0.8384 (m-40) cc_final: 0.7905 (m-40) REVERT: J 302 ILE cc_start: 0.7012 (mm) cc_final: 0.6590 (tp) REVERT: J 314 VAL cc_start: 0.7716 (t) cc_final: 0.7427 (p) REVERT: J 318 LYS cc_start: 0.8258 (mttt) cc_final: 0.7887 (mmmt) REVERT: J 321 ASP cc_start: 0.7988 (t0) cc_final: 0.7498 (t0) REVERT: L 67 VAL cc_start: 0.8960 (t) cc_final: 0.8574 (m) REVERT: L 81 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7247 (mm-30) REVERT: L 103 SER cc_start: 0.7912 (m) cc_final: 0.7550 (p) REVERT: L 151 ASN cc_start: 0.8151 (t0) cc_final: 0.7917 (t0) REVERT: L 158 MET cc_start: 0.5826 (mmm) cc_final: 0.5124 (mmt) REVERT: L 229 LYS cc_start: 0.7658 (ttmt) cc_final: 0.7367 (ttmm) REVERT: F 164 MET cc_start: 0.8278 (tpt) cc_final: 0.7793 (mmm) REVERT: F 168 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6873 (p90) REVERT: F 190 ASP cc_start: 0.9021 (p0) cc_final: 0.8541 (p0) REVERT: F 191 TRP cc_start: 0.8606 (t60) cc_final: 0.8218 (t60) REVERT: F 194 LYS cc_start: 0.7872 (mttt) cc_final: 0.7225 (mmtt) REVERT: F 201 LYS cc_start: 0.8761 (mttt) cc_final: 0.8411 (mmtt) REVERT: F 213 TYR cc_start: 0.6272 (m-80) cc_final: 0.5902 (m-80) REVERT: F 217 TYR cc_start: 0.7520 (p90) cc_final: 0.7183 (p90) outliers start: 71 outliers final: 53 residues processed: 471 average time/residue: 0.1663 time to fit residues: 118.4663 Evaluate side-chains 496 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 435 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 187 GLN Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 218 TYR Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 324 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 69 ASN Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 239 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [145, 172, 103, 165, 25, 24, 17, 57, 42, 134, 151] chunk 145 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 134 optimal weight: 0.0670 chunk 151 optimal weight: 0.0770 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 HIS B 109 ASN E 59 HIS E 137 ASN ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN M 169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.145919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.122322 restraints weight = 62267.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.125916 restraints weight = 34229.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.127746 restraints weight = 18945.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.127946 restraints weight = 14789.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.128173 restraints weight = 13801.747| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23921 Z= 0.166 Angle : 0.720 12.121 33838 Z= 0.392 Chirality : 0.043 0.356 3921 Planarity : 0.005 0.088 3062 Dihedral : 26.210 179.227 6288 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.05 % Allowed : 22.89 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.13 (0.19), residues: 1933 helix: 0.65 (0.16), residues: 1078 sheet: -0.99 (0.39), residues: 195 loop : -0.88 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 267 TYR 0.035 0.002 TYR F 217 PHE 0.017 0.002 PHE E 227 TRP 0.018 0.001 TRP E 47 HIS 0.018 0.001 HIS I 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (23921) covalent geometry : angle 0.71993 / 0.39 (33838) hydrogen bonds : bond 0.05131 / 3.49 ( 1085) hydrogen bonds : angle 4.34622 / 3.07 ( 2868) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 440 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6997 (tpp) cc_final: 0.6386 (tpp) REVERT: A 99 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: A 111 ASN cc_start: 0.8530 (t0) cc_final: 0.8216 (t0) REVERT: A 248 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7521 (mp0) REVERT: A 309 ARG cc_start: 0.8284 (ptm-80) cc_final: 0.7987 (ptm-80) REVERT: A 321 ASP cc_start: 0.8200 (t70) cc_final: 0.7981 (t0) REVERT: B 16 ILE cc_start: 0.9086 (pt) cc_final: 0.8624 (tp) REVERT: B 20 ARG cc_start: 0.8853 (mmm-85) cc_final: 0.8593 (ttt-90) REVERT: B 79 ASP cc_start: 0.8000 (m-30) cc_final: 0.7721 (m-30) REVERT: B 81 GLU cc_start: 0.7580 (pt0) cc_final: 0.6632 (pp20) REVERT: B 103 SER cc_start: 0.9132 (m) cc_final: 0.8693 (p) REVERT: B 105 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7542 (mm-30) REVERT: B 124 LYS cc_start: 0.8875 (pttm) cc_final: 0.8472 (pttm) REVERT: B 164 MET cc_start: 0.8860 (mmm) cc_final: 0.8446 (mmm) REVERT: B 208 ASP cc_start: 0.7829 (t0) cc_final: 0.7400 (p0) REVERT: B 209 ARG cc_start: 0.5446 (mmp-170) cc_final: 0.4976 (mmt180) REVERT: B 235 ASP cc_start: 0.7899 (m-30) cc_final: 0.7423 (m-30) REVERT: E 147 ARG cc_start: 0.6989 (tpt90) cc_final: 0.6722 (tpp-160) REVERT: E 153 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7915 (tp) REVERT: E 201 LYS cc_start: 0.8004 (tttm) cc_final: 0.7617 (tppt) REVERT: E 251 ASN cc_start: 0.7080 (m-40) cc_final: 0.6610 (t0) REVERT: E 259 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8079 (tp) REVERT: E 287 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.6885 (tpp80) REVERT: I 6 GLU cc_start: 0.8592 (tp30) cc_final: 0.8153 (tp30) REVERT: I 9 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7964 (tm-30) REVERT: I 20 ARG cc_start: 0.8393 (mmp80) cc_final: 0.8055 (mmp80) REVERT: I 56 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: I 87 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7305 (tm-30) REVERT: I 107 SER cc_start: 0.8064 (m) cc_final: 0.7787 (t) REVERT: I 109 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: I 149 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8767 (tm-30) REVERT: J 31 PRO cc_start: 0.8226 (Cg_exo) cc_final: 0.7981 (Cg_endo) REVERT: J 57 SER cc_start: 0.8530 (m) cc_final: 0.8205 (p) REVERT: J 187 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7357 (tp-100) REVERT: J 242 ASN cc_start: 0.8370 (m-40) cc_final: 0.7896 (m-40) REVERT: J 302 ILE cc_start: 0.7008 (mm) cc_final: 0.6561 (tp) REVERT: J 314 VAL cc_start: 0.7643 (t) cc_final: 0.7372 (p) REVERT: J 318 LYS cc_start: 0.8300 (mttt) cc_final: 0.7917 (mmmt) REVERT: J 321 ASP cc_start: 0.7997 (t0) cc_final: 0.7488 (t0) REVERT: L 67 VAL cc_start: 0.8966 (t) cc_final: 0.8585 (m) REVERT: L 81 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7278 (mm-30) REVERT: L 103 SER cc_start: 0.7925 (m) cc_final: 0.7556 (p) REVERT: L 119 MET cc_start: 0.7091 (mmm) cc_final: 0.6850 (mmp) REVERT: L 151 ASN cc_start: 0.8165 (t0) cc_final: 0.7941 (t0) REVERT: L 158 MET cc_start: 0.5826 (mmm) cc_final: 0.5151 (mmt) REVERT: L 207 ARG cc_start: 0.5390 (ttt180) cc_final: 0.4730 (ttt180) REVERT: L 229 LYS cc_start: 0.7679 (ttmt) cc_final: 0.7346 (ttmm) REVERT: F 164 MET cc_start: 0.8279 (tpt) cc_final: 0.7799 (mmm) REVERT: F 168 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6880 (p90) REVERT: F 191 TRP cc_start: 0.8584 (t60) cc_final: 0.8153 (t60) REVERT: F 194 LYS cc_start: 0.7862 (mttt) cc_final: 0.7306 (mmtm) REVERT: F 201 LYS cc_start: 0.8784 (mttt) cc_final: 0.7662 (mmtt) REVERT: F 202 LYS cc_start: 0.9335 (mmtt) cc_final: 0.9131 (mtmm) REVERT: F 213 TYR cc_start: 0.6241 (m-80) cc_final: 0.5903 (m-80) outliers start: 71 outliers final: 57 residues processed: 481 average time/residue: 0.1583 time to fit residues: 116.5006 Evaluate side-chains 494 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 429 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 187 GLN Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 218 TYR Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 324 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 69 ASN Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 239 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [15, 131, 31, 220, 13, 9, 85, 77, 174, 209, 64] chunk 15 optimal weight: 0.1980 chunk 131 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 174 optimal weight: 0.0170 chunk 209 optimal weight: 0.2980 chunk 64 optimal weight: 9.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 HIS B 109 ASN E 59 HIS ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 313 HIS L 143 ASN M 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.147184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.123869 restraints weight = 62383.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.127484 restraints weight = 34724.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.128846 restraints weight = 19418.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.129349 restraints weight = 15275.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.129520 restraints weight = 14251.439| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23921 Z= 0.155 Angle : 0.734 11.945 33838 Z= 0.395 Chirality : 0.043 0.355 3921 Planarity : 0.005 0.084 3062 Dihedral : 26.172 179.657 6288 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.20 % Allowed : 24.26 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.06 (0.19), residues: 1933 helix: 0.70 (0.16), residues: 1075 sheet: -0.99 (0.39), residues: 193 loop : -0.81 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 200 TYR 0.037 0.002 TYR F 217 PHE 0.016 0.001 PHE E 227 TRP 0.020 0.001 TRP I 153 HIS 0.017 0.001 HIS I 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (23921) covalent geometry : angle 0.73389 / 0.40 (33838) hydrogen bonds : bond 0.04864 / 3.31 ( 1085) hydrogen bonds : angle 4.29439 / 3.05 ( 2868) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 434 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6982 (tpp) cc_final: 0.6328 (tpp) REVERT: A 99 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7873 (mt0) REVERT: A 111 ASN cc_start: 0.8497 (t0) cc_final: 0.8183 (t0) REVERT: A 309 ARG cc_start: 0.8284 (ptm-80) cc_final: 0.7987 (ptm-80) REVERT: A 321 ASP cc_start: 0.8159 (t70) cc_final: 0.7936 (t0) REVERT: B 16 ILE cc_start: 0.9073 (pt) cc_final: 0.8616 (tp) REVERT: B 20 ARG cc_start: 0.8822 (mmm-85) cc_final: 0.8585 (ttt-90) REVERT: B 79 ASP cc_start: 0.7987 (m-30) cc_final: 0.7651 (m-30) REVERT: B 81 GLU cc_start: 0.7578 (pt0) cc_final: 0.6631 (pp20) REVERT: B 103 SER cc_start: 0.9132 (m) cc_final: 0.8706 (p) REVERT: B 105 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: B 124 LYS cc_start: 0.8887 (pttm) cc_final: 0.8521 (pttm) REVERT: B 147 TYR cc_start: 0.7578 (m-80) cc_final: 0.7284 (m-80) REVERT: B 164 MET cc_start: 0.8878 (mmm) cc_final: 0.8490 (mmm) REVERT: B 208 ASP cc_start: 0.7809 (t0) cc_final: 0.7393 (p0) REVERT: B 209 ARG cc_start: 0.5551 (mmp-170) cc_final: 0.5081 (mmt180) REVERT: B 235 ASP cc_start: 0.7909 (m-30) cc_final: 0.7436 (m-30) REVERT: E 92 ARG cc_start: 0.5858 (OUTLIER) cc_final: 0.4729 (ttt-90) REVERT: E 147 ARG cc_start: 0.6821 (tpt90) cc_final: 0.6613 (tpp-160) REVERT: E 201 LYS cc_start: 0.7965 (tttm) cc_final: 0.7561 (tppt) REVERT: E 251 ASN cc_start: 0.7159 (m-40) cc_final: 0.6683 (t0) REVERT: E 259 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8092 (tp) REVERT: E 287 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.6861 (tpp80) REVERT: I 6 GLU cc_start: 0.8474 (tp30) cc_final: 0.8065 (tp30) REVERT: I 9 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7961 (tm-30) REVERT: I 20 ARG cc_start: 0.8396 (mmp80) cc_final: 0.8177 (mmp80) REVERT: I 39 ARG cc_start: 0.8846 (mmm160) cc_final: 0.8583 (mmm160) REVERT: I 56 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: I 87 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7272 (tm-30) REVERT: I 149 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8815 (tm-30) REVERT: I 154 LEU cc_start: 0.8102 (tt) cc_final: 0.7846 (tp) REVERT: I 165 LYS cc_start: 0.9030 (tppt) cc_final: 0.8763 (ttpp) REVERT: I 170 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6896 (mp0) REVERT: J 31 PRO cc_start: 0.8198 (Cg_exo) cc_final: 0.7941 (Cg_endo) REVERT: J 57 SER cc_start: 0.8584 (m) cc_final: 0.8245 (p) REVERT: J 130 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7324 (pp20) REVERT: J 242 ASN cc_start: 0.8365 (m-40) cc_final: 0.7840 (m-40) REVERT: J 281 ARG cc_start: 0.5433 (mtm180) cc_final: 0.5168 (mtm-85) REVERT: J 314 VAL cc_start: 0.7654 (t) cc_final: 0.7394 (p) REVERT: J 318 LYS cc_start: 0.8265 (mttt) cc_final: 0.7878 (mmmt) REVERT: J 321 ASP cc_start: 0.7998 (t0) cc_final: 0.7497 (t0) REVERT: L 67 VAL cc_start: 0.8964 (t) cc_final: 0.8579 (m) REVERT: L 81 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7282 (mm-30) REVERT: L 103 SER cc_start: 0.7917 (m) cc_final: 0.7534 (p) REVERT: L 119 MET cc_start: 0.6968 (mmm) cc_final: 0.6690 (mmp) REVERT: L 151 ASN cc_start: 0.8187 (t0) cc_final: 0.7957 (t0) REVERT: L 158 MET cc_start: 0.5790 (mmm) cc_final: 0.5430 (mmt) REVERT: L 175 MET cc_start: 0.5783 (mmm) cc_final: 0.4895 (tpp) REVERT: L 229 LYS cc_start: 0.7664 (ttmt) cc_final: 0.7319 (ttmm) REVERT: F 164 MET cc_start: 0.8247 (tpt) cc_final: 0.7770 (mmm) REVERT: F 168 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6881 (p90) REVERT: F 191 TRP cc_start: 0.8530 (t60) cc_final: 0.8138 (t60) REVERT: F 194 LYS cc_start: 0.7855 (mttt) cc_final: 0.7479 (mtmm) REVERT: F 201 LYS cc_start: 0.8663 (mttt) cc_final: 0.7878 (mmtt) REVERT: F 202 LYS cc_start: 0.9269 (mmtt) cc_final: 0.9049 (mtmm) REVERT: F 213 TYR cc_start: 0.6314 (m-80) cc_final: 0.5965 (m-80) outliers start: 56 outliers final: 47 residues processed: 467 average time/residue: 0.1637 time to fit residues: 115.8462 Evaluate side-chains 480 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 427 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 218 TYR Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 324 ASN Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 69 ASN Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 239 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [85, 95, 157, 212, 220, 112, 64, 60, 219, 114, 149] chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 0.0470 chunk 157 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 220 optimal weight: 0.4980 chunk 112 optimal weight: 0.3980 chunk 64 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 219 optimal weight: 0.0670 chunk 114 optimal weight: 3.9990 chunk 149 optimal weight: 0.0060 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 HIS E 59 HIS ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.148073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.124749 restraints weight = 62799.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.128586 restraints weight = 34650.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.129727 restraints weight = 19126.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.130393 restraints weight = 15242.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.130430 restraints weight = 14302.588| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23921 Z= 0.150 Angle : 0.714 12.055 33838 Z= 0.386 Chirality : 0.042 0.354 3921 Planarity : 0.005 0.082 3062 Dihedral : 26.121 179.875 6288 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.91 % Allowed : 24.60 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: 0.02 (0.19), residues: 1933 helix: 0.76 (0.16), residues: 1080 sheet: -0.93 (0.39), residues: 193 loop : -0.79 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 267 TYR 0.034 0.001 TYR F 217 PHE 0.014 0.001 PHE M 32 TRP 0.015 0.001 TRP I 153 HIS 0.019 0.001 HIS I 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (23921) covalent geometry : angle 0.71375 / 0.39 (33838) hydrogen bonds : bond 0.04682 / 3.20 ( 1085) hydrogen bonds : angle 4.25899 / 3.02 ( 2868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4170.21 seconds wall clock time: 72 minutes 42.05 seconds (4362.05 seconds total)