Starting phenix.real_space_refine on Mon Jul 6 02:38:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbm_13295/07_2026/7pbm_13295_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbm_13295/07_2026/7pbm_13295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pbm_13295/07_2026/7pbm_13295_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbm_13295/07_2026/7pbm_13295_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbm_13295/07_2026/7pbm_13295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbm_13295/07_2026/7pbm_13295.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 45 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 10134 2.51 5 N 2757 2.21 5 O 3220 1.98 5 H 15819 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32079 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 760 Classifications: {'peptide': 50} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "U" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 480 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.17 Number of scatterers: 32079 At special positions: 0 Unit cell: (125.35, 137.34, 107.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 45 15.00 Mg 3 11.99 O 3220 8.00 N 2757 7.00 C 10134 6.00 H 15819 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 877.9 milliseconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 20 sheets defined 59.1% alpha, 10.9% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 4.62 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.554A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.606A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.542A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.925A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.806A pdb=" N MET A 163 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.670A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 Processing helix chain 'A' and resid 216 through 234 removed outlier: 3.551A pdb=" N GLN A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.868A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 removed outlier: 3.610A pdb=" N GLY A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.626A pdb=" N GLU A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.782A pdb=" N LEU A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.637A pdb=" N MET A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.568A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.671A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.564A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.916A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 216 through 234 Processing helix chain 'B' and resid 240 through 251 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.799A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.624A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.525A pdb=" N HIS B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 31 through 49 Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.753A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.584A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.575A pdb=" N GLU C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.534A pdb=" N ALA C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.590A pdb=" N GLU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 212 removed outlier: 3.581A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 234 removed outlier: 3.531A pdb=" N TYR C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.657A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 273 removed outlier: 3.554A pdb=" N LEU C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 290 through 298 removed outlier: 3.504A pdb=" N GLU C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.860A pdb=" N LEU C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.532A pdb=" N TYR D 28 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.727A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 77 Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.729A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 129 removed outlier: 4.673A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 182 through 194 removed outlier: 4.457A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 216 through 232 removed outlier: 3.525A pdb=" N ARG D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 251 removed outlier: 3.515A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 279 through 288 removed outlier: 3.687A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.576A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'E' and resid 31 through 48 removed outlier: 3.627A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.643A pdb=" N PHE E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.683A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.614A pdb=" N GLU E 120 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.501A pdb=" N ILE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 213 removed outlier: 3.769A pdb=" N LEU E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 234 removed outlier: 3.927A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 removed outlier: 3.596A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 279 through 287 Processing helix chain 'E' and resid 290 through 298 removed outlier: 3.622A pdb=" N ASP E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 removed outlier: 3.557A pdb=" N LEU E 302 " --> pdb=" O TYR E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.504A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.593A pdb=" N PHE F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 90 through 99 removed outlier: 3.784A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.529A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU F 128 " --> pdb=" O TYR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 165 through 170 removed outlier: 3.557A pdb=" N ALA F 170 " --> pdb=" O ASN F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 197 Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 216 through 234 removed outlier: 4.084A pdb=" N ASP F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.891A pdb=" N GLU F 271 " --> pdb=" O ARG F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 288 Processing helix chain 'F' and resid 290 through 298 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 318 through 326 removed outlier: 3.638A pdb=" N TYR F 322 " --> pdb=" O THR F 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 190 through 202 Processing helix chain 'H' and resid 159 through 170 Processing helix chain 'H' and resid 173 through 184 removed outlier: 3.700A pdb=" N ILE H 184 " --> pdb=" O MET H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 199 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.548A pdb=" N ASP A 110 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 136 removed outlier: 3.506A pdb=" N ILE A 136 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 removed outlier: 7.146A pdb=" N THR A 200 " --> pdb=" O ILE A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 84 removed outlier: 6.442A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 84 removed outlier: 3.515A pdb=" N ASP C 110 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 56 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.244A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR D 55 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N THR D 158 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU D 57 " --> pdb=" O THR D 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AB5, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.559A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU E 56 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 131 through 136 Processing sheet with id=AB7, first strand: chain 'E' and resid 200 through 201 removed outlier: 7.056A pdb=" N THR E 200 " --> pdb=" O ILE E 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 308 through 311 Processing sheet with id=AB9, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.401A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 131 through 136 removed outlier: 3.521A pdb=" N ILE F 134 " --> pdb=" O VAL F 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 308 through 311 766 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 7.01 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 15819 1.06 - 1.28: 2721 1.28 - 1.50: 6908 1.50 - 1.72: 6779 1.72 - 1.94: 199 Bond restraints: 32426 Sorted by residual: bond pdb=" N THR F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N SER G 156 " pdb=" H1 SER G 156 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR A 19 " pdb=" H1 THR A 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 32421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 57984 2.04 - 4.08: 615 4.08 - 6.13: 66 6.13 - 8.17: 13 8.17 - 10.21: 14 Bond angle restraints: 58692 Sorted by residual: angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 111.07 -3.07 7.00e-01 2.04e+00 1.92e+01 angle pdb=" N PHE B 197 " pdb=" CA PHE B 197 " pdb=" C PHE B 197 " ideal model delta sigma weight residual 110.41 105.10 5.31 1.23e+00 6.61e-01 1.86e+01 angle pdb=" N3 DT U 7 " pdb=" C4 DT U 7 " pdb=" O4 DT U 7 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT V 3 " pdb=" C4 DT V 3 " pdb=" O4 DT V 3 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT V 4 " pdb=" C4 DT V 4 " pdb=" O4 DT V 4 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+01 ... (remaining 58687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.07: 14461 32.07 - 64.14: 582 64.14 - 96.21: 45 96.21 - 128.28: 1 128.28 - 160.35: 5 Dihedral angle restraints: 15094 sinusoidal: 8661 harmonic: 6433 Sorted by residual: dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 100.36 -160.35 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 86.89 -146.89 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 76.64 -136.65 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 15091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2296 0.079 - 0.157: 240 0.157 - 0.236: 8 0.236 - 0.315: 3 0.315 - 0.393: 1 Chirality restraints: 2548 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.73 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C3' AGS B 401 " pdb=" C2' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" O3' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3' AGS A 401 " pdb=" C2' AGS A 401 " pdb=" C4' AGS A 401 " pdb=" O3' AGS A 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2545 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.156 9.50e-02 1.11e+02 7.14e-02 5.63e+01 pdb=" NE ARG C 192 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.057 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.082 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.067 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 312 " -0.445 9.50e-02 1.11e+02 1.53e-01 5.48e+01 pdb=" NE ARG F 312 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 312 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG F 312 " 0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG F 312 " 0.062 2.00e-02 2.50e+03 pdb="HH11 ARG F 312 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG F 312 " -0.037 2.00e-02 2.50e+03 pdb="HH21 ARG F 312 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG F 312 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.044 2.00e-02 2.50e+03 5.51e-02 4.55e+01 pdb=" CD GLN C 31 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.088 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.003 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.085 2.00e-02 2.50e+03 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1058 2.17 - 2.78: 60711 2.78 - 3.39: 82482 3.39 - 3.99: 107541 3.99 - 4.60: 172414 Nonbonded interactions: 424206 Sorted by model distance: nonbonded pdb="HH21 ARG E 312 " pdb=" OP1 DA V 10 " model vdw 1.564 2.450 nonbonded pdb=" OE2 GLU C 128 " pdb="HH22 ARG D 218 " model vdw 1.570 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.570 2.450 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.591 2.450 nonbonded pdb=" O ALA F 138 " pdb=" HG1 THR F 141 " model vdw 1.593 2.450 ... (remaining 424201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } ncs_group { reference = (chain 'G' and (resid 158 through 202 or (resid 203 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name H or name H \ A or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or n \ ame HD21 or name HD22 or name HD23)))) selection = (chain 'H' and resid 158 through 203) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.770 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 16607 Z= 0.255 Angle : 0.782 10.210 22614 Z= 0.452 Chirality : 0.047 0.393 2548 Planarity : 0.011 0.154 2808 Dihedral : 15.620 160.355 6466 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.06 % Allowed : 1.28 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -1.25 (0.18), residues: 1950 helix: -1.47 (0.14), residues: 1035 sheet: 0.35 (0.30), residues: 298 loop : 0.22 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG C 114 TYR 0.033 0.005 TYR F 131 PHE 0.019 0.003 PHE F 25 HIS 0.011 0.003 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.25 (16607) covalent geometry : angle 0.78236 / 0.45 (22614) hydrogen bonds : bond 0.26593 / 17.87 ( 793) hydrogen bonds : angle 8.53690 / 5.93 ( 2241) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 0.607 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 76 MET cc_start: 0.9007 (mmm) cc_final: 0.8648 (mmt) REVERT: A 79 ASN cc_start: 0.7865 (m-40) cc_final: 0.7274 (m-40) REVERT: A 110 ASP cc_start: 0.8071 (t0) cc_final: 0.7844 (t70) REVERT: A 178 MET cc_start: 0.9017 (mmm) cc_final: 0.8766 (mmt) REVERT: A 222 ARG cc_start: 0.7838 (ttp-170) cc_final: 0.7478 (ttm170) REVERT: A 309 MET cc_start: 0.7229 (ttm) cc_final: 0.7017 (ttp) REVERT: C 121 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 144 SER cc_start: 0.6230 (p) cc_final: 0.5753 (p) REVERT: C 178 MET cc_start: 0.9112 (mmt) cc_final: 0.8637 (mmt) REVERT: C 234 MET cc_start: 0.8723 (mmt) cc_final: 0.8435 (mmt) REVERT: C 325 MET cc_start: 0.9365 (mmm) cc_final: 0.9162 (mmp) REVERT: D 105 ASP cc_start: 0.7600 (m-30) cc_final: 0.7169 (m-30) REVERT: E 105 ASP cc_start: 0.6662 (m-30) cc_final: 0.6107 (m-30) REVERT: E 330 THR cc_start: 0.7829 (m) cc_final: 0.7548 (p) REVERT: F 102 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7400 (mm-30) REVERT: F 298 TYR cc_start: 0.7431 (m-80) cc_final: 0.7200 (m-80) REVERT: H 200 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7509 (mmm-85) outliers start: 1 outliers final: 1 residues processed: 428 average time/residue: 0.3189 time to fit residues: 190.9983 Evaluate side-chains 263 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 286 ASN E 304 GLN G 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.099874 restraints weight = 66829.941| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.25 r_work: 0.2925 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 16607 Z= 0.185 Angle : 0.665 6.571 22614 Z= 0.363 Chirality : 0.044 0.157 2548 Planarity : 0.006 0.051 2808 Dihedral : 15.203 168.848 2653 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.73 % Allowed : 6.40 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.09 (0.18), residues: 1950 helix: -0.14 (0.16), residues: 1062 sheet: 0.46 (0.31), residues: 277 loop : 0.22 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 48 TYR 0.027 0.001 TYR C 124 PHE 0.009 0.001 PHE D 70 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (16607) covalent geometry : angle 0.66531 / 0.36 (22614) hydrogen bonds : bond 0.07864 / 5.26 ( 793) hydrogen bonds : angle 5.86347 / 4.10 ( 2241) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 273 time to evaluate : 0.765 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: A 68 MET cc_start: 0.9186 (tpp) cc_final: 0.8817 (tpp) REVERT: A 76 MET cc_start: 0.8996 (mmm) cc_final: 0.8722 (mmt) REVERT: A 79 ASN cc_start: 0.8419 (m-40) cc_final: 0.7845 (m-40) REVERT: A 110 ASP cc_start: 0.8708 (t0) cc_final: 0.8507 (t70) REVERT: A 178 MET cc_start: 0.9236 (mmm) cc_final: 0.9022 (mmt) REVERT: A 199 MET cc_start: 0.7861 (mmt) cc_final: 0.7594 (mmt) REVERT: A 222 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.7773 (ttm170) REVERT: A 309 MET cc_start: 0.8177 (ttm) cc_final: 0.7885 (ttp) REVERT: C 110 ASP cc_start: 0.8735 (t0) cc_final: 0.8471 (m-30) REVERT: C 121 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7875 (mt-10) REVERT: C 147 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7321 (mp) REVERT: C 178 MET cc_start: 0.9238 (mmt) cc_final: 0.8731 (mmt) REVERT: E 81 LYS cc_start: 0.8367 (mttt) cc_final: 0.7623 (tptt) REVERT: E 105 ASP cc_start: 0.7990 (m-30) cc_final: 0.7788 (m-30) REVERT: E 127 MET cc_start: 0.8077 (mtp) cc_final: 0.7727 (mtm) REVERT: E 272 MET cc_start: 0.8159 (mtt) cc_final: 0.7931 (mtt) REVERT: E 325 MET cc_start: 0.7168 (mmm) cc_final: 0.6913 (mmp) REVERT: E 330 THR cc_start: 0.7861 (m) cc_final: 0.7551 (p) REVERT: F 234 MET cc_start: 0.7742 (ttm) cc_final: 0.7522 (ttm) REVERT: F 252 ASP cc_start: 0.7955 (m-30) cc_final: 0.7347 (p0) REVERT: H 200 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7612 (mtp-110) outliers start: 12 outliers final: 8 residues processed: 280 average time/residue: 0.3100 time to fit residues: 122.9680 Evaluate side-chains 253 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 244 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain H residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 107 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.098022 restraints weight = 66915.239| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.24 r_work: 0.2977 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16607 Z= 0.208 Angle : 0.610 6.320 22614 Z= 0.328 Chirality : 0.043 0.244 2548 Planarity : 0.005 0.050 2808 Dihedral : 14.910 166.269 2653 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.16 % Allowed : 7.37 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.01 (0.19), residues: 1950 helix: 0.11 (0.16), residues: 1064 sheet: 0.26 (0.31), residues: 275 loop : -0.01 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 179 TYR 0.024 0.001 TYR C 124 PHE 0.008 0.001 PHE C 152 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (16607) covalent geometry : angle 0.61033 / 0.33 (22614) hydrogen bonds : bond 0.07141 / 4.78 ( 793) hydrogen bonds : angle 5.44617 / 3.83 ( 2241) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.894 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 76 MET cc_start: 0.9001 (mmm) cc_final: 0.8742 (mmt) REVERT: A 79 ASN cc_start: 0.8419 (m-40) cc_final: 0.7864 (m-40) REVERT: A 222 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.7845 (ttm170) REVERT: A 309 MET cc_start: 0.8208 (ttm) cc_final: 0.7957 (ttp) REVERT: C 110 ASP cc_start: 0.8666 (t0) cc_final: 0.8430 (m-30) REVERT: C 121 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7914 (mt-10) REVERT: C 147 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7505 (mp) REVERT: C 178 MET cc_start: 0.9289 (mmt) cc_final: 0.8818 (mmt) REVERT: E 81 LYS cc_start: 0.8478 (mttt) cc_final: 0.7794 (tptt) REVERT: E 272 MET cc_start: 0.8125 (mtt) cc_final: 0.7886 (mtt) REVERT: E 325 MET cc_start: 0.7392 (mmm) cc_final: 0.7178 (mmp) REVERT: E 330 THR cc_start: 0.8020 (m) cc_final: 0.7744 (p) REVERT: F 252 ASP cc_start: 0.7978 (m-30) cc_final: 0.7417 (p0) REVERT: F 310 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7528 (tpp80) REVERT: H 200 ARG cc_start: 0.8166 (ttt180) cc_final: 0.7670 (mtp-110) outliers start: 19 outliers final: 15 residues processed: 266 average time/residue: 0.3035 time to fit residues: 115.2872 Evaluate side-chains 261 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 245 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 125 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097097 restraints weight = 66963.946| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.24 r_work: 0.2915 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16607 Z= 0.202 Angle : 0.590 6.138 22614 Z= 0.314 Chirality : 0.042 0.143 2548 Planarity : 0.005 0.075 2808 Dihedral : 14.726 165.009 2653 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.46 % Allowed : 8.04 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.05 (0.19), residues: 1950 helix: 0.28 (0.16), residues: 1071 sheet: 0.10 (0.30), residues: 275 loop : -0.14 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 143 TYR 0.022 0.001 TYR C 124 PHE 0.009 0.001 PHE C 152 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (16607) covalent geometry : angle 0.59037 / 0.31 (22614) hydrogen bonds : bond 0.06047 / 4.02 ( 793) hydrogen bonds : angle 5.11200 / 3.60 ( 2241) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 0.625 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: A 79 ASN cc_start: 0.8388 (m-40) cc_final: 0.7846 (m-40) REVERT: A 222 ARG cc_start: 0.8301 (ttp-170) cc_final: 0.7923 (ttm170) REVERT: A 309 MET cc_start: 0.8287 (ttm) cc_final: 0.7978 (ttp) REVERT: C 110 ASP cc_start: 0.8702 (t0) cc_final: 0.8449 (m-30) REVERT: C 121 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7938 (mt-10) REVERT: C 147 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7503 (mp) REVERT: C 178 MET cc_start: 0.9274 (mmt) cc_final: 0.8805 (mmt) REVERT: D 39 LYS cc_start: 0.8214 (tttt) cc_final: 0.7965 (tptp) REVERT: E 81 LYS cc_start: 0.8516 (mttt) cc_final: 0.7748 (tptt) REVERT: E 272 MET cc_start: 0.8197 (mtt) cc_final: 0.7939 (mtt) REVERT: E 330 THR cc_start: 0.8135 (m) cc_final: 0.7824 (p) REVERT: F 84 SER cc_start: 0.8856 (p) cc_final: 0.8629 (t) REVERT: F 252 ASP cc_start: 0.8056 (m-30) cc_final: 0.7371 (p0) REVERT: F 296 ASP cc_start: 0.7572 (m-30) cc_final: 0.7334 (m-30) REVERT: H 200 ARG cc_start: 0.8113 (ttt180) cc_final: 0.7621 (mtp-110) outliers start: 24 outliers final: 16 residues processed: 262 average time/residue: 0.3107 time to fit residues: 116.0202 Evaluate side-chains 261 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 161 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.098957 restraints weight = 66732.206| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.16 r_work: 0.2978 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16607 Z= 0.147 Angle : 0.544 6.213 22614 Z= 0.288 Chirality : 0.040 0.133 2548 Planarity : 0.005 0.055 2808 Dihedral : 14.526 165.625 2653 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.28 % Allowed : 8.41 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1950 helix: 0.52 (0.16), residues: 1070 sheet: 0.11 (0.30), residues: 281 loop : -0.05 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 169 TYR 0.021 0.001 TYR C 124 PHE 0.007 0.001 PHE A 58 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16607) covalent geometry : angle 0.54396 / 0.29 (22614) hydrogen bonds : bond 0.05312 / 3.54 ( 793) hydrogen bonds : angle 4.87343 / 3.43 ( 2241) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 0.892 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: A 79 ASN cc_start: 0.8347 (m-40) cc_final: 0.7811 (m-40) REVERT: A 222 ARG cc_start: 0.8294 (ttp-170) cc_final: 0.7951 (ttm170) REVERT: A 286 ASN cc_start: 0.7746 (m110) cc_final: 0.7517 (m110) REVERT: A 309 MET cc_start: 0.8166 (ttm) cc_final: 0.7900 (ttp) REVERT: C 110 ASP cc_start: 0.8651 (t0) cc_final: 0.8385 (m-30) REVERT: C 147 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7517 (mp) REVERT: C 178 MET cc_start: 0.9237 (mmt) cc_final: 0.8691 (mmt) REVERT: E 81 LYS cc_start: 0.8502 (mttt) cc_final: 0.7792 (tptt) REVERT: E 272 MET cc_start: 0.8209 (mtt) cc_final: 0.7950 (mtt) REVERT: E 330 THR cc_start: 0.8123 (m) cc_final: 0.7834 (p) REVERT: F 252 ASP cc_start: 0.7955 (m-30) cc_final: 0.7317 (p0) REVERT: H 200 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7658 (mtp-110) outliers start: 21 outliers final: 17 residues processed: 261 average time/residue: 0.3402 time to fit residues: 126.6189 Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.098735 restraints weight = 66586.891| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.17 r_work: 0.3001 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16607 Z= 0.158 Angle : 0.541 6.267 22614 Z= 0.285 Chirality : 0.040 0.131 2548 Planarity : 0.005 0.070 2808 Dihedral : 14.442 163.905 2653 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.16 % Allowed : 8.65 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.42 (0.19), residues: 1950 helix: 0.65 (0.16), residues: 1071 sheet: 0.13 (0.30), residues: 281 loop : -0.04 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 160 TYR 0.021 0.001 TYR C 124 PHE 0.007 0.001 PHE C 152 HIS 0.011 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (16607) covalent geometry : angle 0.54118 / 0.29 (22614) hydrogen bonds : bond 0.05099 / 3.39 ( 793) hydrogen bonds : angle 4.74991 / 3.34 ( 2241) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.869 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: A 79 ASN cc_start: 0.8322 (m-40) cc_final: 0.7784 (m-40) REVERT: A 222 ARG cc_start: 0.8316 (ttp-170) cc_final: 0.7957 (ttm170) REVERT: A 309 MET cc_start: 0.8250 (ttm) cc_final: 0.7968 (ttp) REVERT: C 147 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7508 (mp) REVERT: C 178 MET cc_start: 0.9224 (mmt) cc_final: 0.8792 (mmt) REVERT: D 135 MET cc_start: 0.7731 (mmm) cc_final: 0.7417 (mmt) REVERT: E 81 LYS cc_start: 0.8532 (mttt) cc_final: 0.7774 (tptt) REVERT: E 272 MET cc_start: 0.8185 (mtt) cc_final: 0.7943 (mtt) REVERT: E 330 THR cc_start: 0.8151 (m) cc_final: 0.7859 (p) REVERT: F 252 ASP cc_start: 0.7860 (m-30) cc_final: 0.7251 (p0) REVERT: H 200 ARG cc_start: 0.8108 (ttt180) cc_final: 0.7627 (mtp-110) outliers start: 19 outliers final: 15 residues processed: 252 average time/residue: 0.3135 time to fit residues: 112.7112 Evaluate side-chains 253 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 97 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 86 optimal weight: 0.4980 chunk 81 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.125813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100487 restraints weight = 66880.370| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.03 r_work: 0.3019 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16607 Z= 0.123 Angle : 0.518 6.283 22614 Z= 0.272 Chirality : 0.040 0.127 2548 Planarity : 0.004 0.050 2808 Dihedral : 14.353 164.955 2653 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.98 % Allowed : 9.20 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.63 (0.19), residues: 1950 helix: 0.81 (0.16), residues: 1073 sheet: 0.19 (0.30), residues: 281 loop : 0.08 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.019 0.001 TYR C 124 PHE 0.007 0.001 PHE A 58 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (16607) covalent geometry : angle 0.51814 / 0.27 (22614) hydrogen bonds : bond 0.04611 / 3.07 ( 793) hydrogen bonds : angle 4.60003 / 3.23 ( 2241) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.966 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: A 79 ASN cc_start: 0.8292 (m-40) cc_final: 0.7761 (m-40) REVERT: A 222 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.7947 (ttm170) REVERT: A 309 MET cc_start: 0.8200 (ttm) cc_final: 0.7929 (ttp) REVERT: C 147 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7542 (mp) REVERT: C 178 MET cc_start: 0.9197 (mmt) cc_final: 0.8757 (mmt) REVERT: D 135 MET cc_start: 0.7479 (mmm) cc_final: 0.7185 (mmt) REVERT: E 81 LYS cc_start: 0.8526 (mttt) cc_final: 0.7776 (tptt) REVERT: E 117 MET cc_start: 0.7281 (tpp) cc_final: 0.7033 (tpt) REVERT: E 272 MET cc_start: 0.8122 (mtt) cc_final: 0.7895 (mtt) REVERT: E 330 THR cc_start: 0.8143 (m) cc_final: 0.7859 (p) REVERT: H 200 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7599 (mtp-110) outliers start: 16 outliers final: 11 residues processed: 248 average time/residue: 0.3119 time to fit residues: 110.3481 Evaluate side-chains 251 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 166 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.095911 restraints weight = 67472.023| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.16 r_work: 0.2908 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 16607 Z= 0.239 Angle : 0.590 6.252 22614 Z= 0.312 Chirality : 0.043 0.143 2548 Planarity : 0.005 0.073 2808 Dihedral : 14.452 155.776 2653 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.04 % Allowed : 9.45 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.34 (0.19), residues: 1950 helix: 0.65 (0.16), residues: 1070 sheet: 0.06 (0.30), residues: 281 loop : -0.21 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 160 TYR 0.022 0.002 TYR C 124 PHE 0.011 0.001 PHE C 152 HIS 0.008 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 (16607) covalent geometry : angle 0.58976 / 0.31 (22614) hydrogen bonds : bond 0.05673 / 3.76 ( 793) hydrogen bonds : angle 4.77520 / 3.35 ( 2241) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.879 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: A 79 ASN cc_start: 0.8315 (m-40) cc_final: 0.7837 (m110) REVERT: A 222 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.7968 (ttm170) REVERT: A 309 MET cc_start: 0.8286 (ttm) cc_final: 0.7971 (ttp) REVERT: C 110 ASP cc_start: 0.8696 (t0) cc_final: 0.8432 (m-30) REVERT: C 147 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7550 (mp) REVERT: C 178 MET cc_start: 0.9243 (mmt) cc_final: 0.8823 (mmt) REVERT: E 81 LYS cc_start: 0.8487 (mttt) cc_final: 0.7778 (tptt) REVERT: E 117 MET cc_start: 0.7358 (tpp) cc_final: 0.7144 (tpt) REVERT: E 272 MET cc_start: 0.8251 (mtt) cc_final: 0.8010 (mtt) REVERT: E 330 THR cc_start: 0.8145 (m) cc_final: 0.7861 (p) REVERT: F 252 ASP cc_start: 0.7943 (m-30) cc_final: 0.7333 (p0) REVERT: H 200 ARG cc_start: 0.8136 (ttt180) cc_final: 0.7663 (mtp-110) outliers start: 17 outliers final: 12 residues processed: 251 average time/residue: 0.3024 time to fit residues: 107.8087 Evaluate side-chains 254 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 175 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 116 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 107 optimal weight: 0.0040 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN B 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099197 restraints weight = 65924.320| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.15 r_work: 0.3024 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16607 Z= 0.110 Angle : 0.521 6.336 22614 Z= 0.273 Chirality : 0.039 0.131 2548 Planarity : 0.005 0.064 2808 Dihedral : 14.352 161.152 2653 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.85 % Allowed : 9.93 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.70 (0.19), residues: 1950 helix: 0.91 (0.16), residues: 1073 sheet: 0.11 (0.30), residues: 281 loop : 0.06 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 291 TYR 0.017 0.001 TYR C 124 PHE 0.007 0.001 PHE E 25 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (16607) covalent geometry : angle 0.52127 / 0.27 (22614) hydrogen bonds : bond 0.04445 / 2.96 ( 793) hydrogen bonds : angle 4.54289 / 3.19 ( 2241) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 247 time to evaluate : 0.829 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: A 79 ASN cc_start: 0.8308 (m-40) cc_final: 0.7787 (m-40) REVERT: A 222 ARG cc_start: 0.8316 (ttp-170) cc_final: 0.7946 (ttm170) REVERT: A 309 MET cc_start: 0.8265 (ttm) cc_final: 0.7977 (ttp) REVERT: B 105 ASP cc_start: 0.8851 (m-30) cc_final: 0.8611 (t0) REVERT: C 90 LYS cc_start: 0.8234 (pttt) cc_final: 0.7960 (mtmm) REVERT: C 110 ASP cc_start: 0.8637 (t0) cc_final: 0.8355 (m-30) REVERT: C 147 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7590 (mp) REVERT: D 39 LYS cc_start: 0.8193 (tttt) cc_final: 0.7922 (tptp) REVERT: D 135 MET cc_start: 0.7669 (mmm) cc_final: 0.7348 (mmt) REVERT: E 81 LYS cc_start: 0.8394 (mttt) cc_final: 0.7752 (tptt) REVERT: E 117 MET cc_start: 0.7318 (tpp) cc_final: 0.7112 (tpt) REVERT: E 272 MET cc_start: 0.8074 (mtt) cc_final: 0.7839 (mtt) REVERT: E 330 THR cc_start: 0.8105 (m) cc_final: 0.7817 (p) REVERT: H 200 ARG cc_start: 0.8057 (ttt180) cc_final: 0.7592 (mtp-110) outliers start: 14 outliers final: 9 residues processed: 253 average time/residue: 0.3140 time to fit residues: 113.3708 Evaluate side-chains 252 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 242 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 27 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN B 286 ASN D 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.097615 restraints weight = 66836.578| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.15 r_work: 0.2997 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16607 Z= 0.145 Angle : 0.530 6.232 22614 Z= 0.277 Chirality : 0.040 0.126 2548 Planarity : 0.005 0.069 2808 Dihedral : 14.335 159.267 2653 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.67 % Allowed : 10.48 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.72 (0.19), residues: 1950 helix: 0.94 (0.16), residues: 1073 sheet: 0.11 (0.30), residues: 280 loop : 0.03 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 160 TYR 0.020 0.001 TYR C 124 PHE 0.006 0.001 PHE C 152 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (16607) covalent geometry : angle 0.53043 / 0.28 (22614) hydrogen bonds : bond 0.04640 / 3.08 ( 793) hydrogen bonds : angle 4.54003 / 3.18 ( 2241) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 244 time to evaluate : 0.999 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: A 79 ASN cc_start: 0.8294 (m-40) cc_final: 0.7767 (m-40) REVERT: A 222 ARG cc_start: 0.8322 (ttp-170) cc_final: 0.7944 (ttm170) REVERT: A 309 MET cc_start: 0.8319 (ttm) cc_final: 0.8024 (ttp) REVERT: B 105 ASP cc_start: 0.8856 (m-30) cc_final: 0.8620 (t0) REVERT: C 110 ASP cc_start: 0.8663 (t0) cc_final: 0.8372 (m-30) REVERT: C 147 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7475 (mp) REVERT: C 178 MET cc_start: 0.9246 (mmt) cc_final: 0.8821 (mmt) REVERT: D 39 LYS cc_start: 0.8174 (tttt) cc_final: 0.7853 (tptp) REVERT: D 135 MET cc_start: 0.7717 (mmm) cc_final: 0.7395 (mmt) REVERT: E 81 LYS cc_start: 0.8421 (mttt) cc_final: 0.7758 (tptt) REVERT: E 117 MET cc_start: 0.7335 (tpp) cc_final: 0.7133 (tpt) REVERT: E 272 MET cc_start: 0.8175 (mtt) cc_final: 0.7947 (mtt) REVERT: E 330 THR cc_start: 0.8123 (m) cc_final: 0.7836 (p) REVERT: H 197 ASP cc_start: 0.7779 (m-30) cc_final: 0.7502 (p0) REVERT: H 200 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7593 (mtp-110) outliers start: 11 outliers final: 10 residues processed: 248 average time/residue: 0.3569 time to fit residues: 125.9386 Evaluate side-chains 255 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 244 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 26 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 131 optimal weight: 0.1980 chunk 146 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN B 79 ASN D 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.098480 restraints weight = 66395.127| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.14 r_work: 0.2978 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.319 16607 Z= 0.215 Angle : 0.729 58.761 22614 Z= 0.421 Chirality : 0.042 0.752 2548 Planarity : 0.005 0.068 2808 Dihedral : 14.334 159.289 2653 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.85 % Allowed : 10.54 % Favored : 88.60 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.82 % 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: 0.72 (0.19), residues: 1950 helix: 0.95 (0.16), residues: 1073 sheet: 0.11 (0.30), residues: 280 loop : 0.03 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 160 TYR 0.020 0.001 TYR C 124 PHE 0.006 0.001 PHE A 58 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (16607) covalent geometry : angle 0.72931 / 0.42 (22614) hydrogen bonds : bond 0.04613 / 3.07 ( 793) hydrogen bonds : angle 4.53995 / 3.18 ( 2241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7113.56 seconds wall clock time: 121 minutes 3.28 seconds (7263.28 seconds total)