Starting phenix.real_space_refine on Fri Mar 6 15:34:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbm_13295/03_2026/7pbm_13295_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbm_13295/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbm_13295/03_2026/7pbm_13295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbm_13295/03_2026/7pbm_13295.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbm_13295/03_2026/7pbm_13295_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbm_13295/03_2026/7pbm_13295_neut_trim.cif" } 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-5986/lib/python3.9/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: 4.85, per 1000 atoms: 0.15 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: 2.50 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 5.26 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: 7.03 Time building geometry restraints manager: 3.35 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 - 2.03: 58069 2.03 - 4.07: 565 4.07 - 6.10: 49 6.10 - 8.13: 5 8.13 - 10.17: 4 Bond angle restraints: 58692 Sorted by residual: 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=" CA TYR C 124 " pdb=" CB TYR C 124 " pdb=" CG TYR C 124 " ideal model delta sigma weight residual 113.90 120.24 -6.34 1.80e+00 3.09e-01 1.24e+01 angle pdb=" N PHE D 197 " pdb=" CA PHE D 197 " pdb=" C PHE D 197 " ideal model delta sigma weight residual 110.41 106.11 4.30 1.23e+00 6.61e-01 1.22e+01 angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.83 10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 117.22 -9.22 3.00e+00 1.11e-01 9.44e+00 ... (remaining 58687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.07: 14436 32.07 - 64.14: 566 64.14 - 96.21: 32 96.21 - 128.28: 2 128.28 - 160.35: 4 Dihedral angle restraints: 15040 sinusoidal: 8607 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 15037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2317 0.077 - 0.153: 233 0.153 - 0.230: 3 0.230 - 0.306: 0 0.306 - 0.383: 1 Chirality restraints: 2554 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 2.35 -2.73 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA TYR C 124 " pdb=" N TYR C 124 " pdb=" C TYR C 124 " pdb=" CB TYR C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA ARG E 214 " pdb=" N ARG E 214 " pdb=" C ARG E 214 " pdb=" CB ARG E 214 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 2551 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.980 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 0.004 0.040 16607 Z= 0.168 Angle : 0.716 10.167 22614 Z= 0.409 Chirality : 0.044 0.383 2554 Planarity : 0.011 0.154 2808 Dihedral : 14.991 160.355 6412 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 covalent geometry : bond 0.00391 (16607) covalent geometry : angle 0.71650 (22614) hydrogen bonds : bond 0.26593 ( 793) hydrogen bonds : angle 8.53690 ( 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 : 0.872 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: 0.3555 time to fit residues: 209.7646 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 : 0.961 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 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: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3501 r_free = 0.3501 target = 0.125744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.098230 restraints weight = 67115.812| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.26 r_work: 0.2944 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16607 Z= 0.191 Angle : 0.647 6.460 22614 Z= 0.352 Chirality : 0.042 0.136 2554 Planarity : 0.005 0.043 2808 Dihedral : 14.511 147.036 2599 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.79 % Allowed : 6.52 % Favored : 92.69 % 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: -0.10 (0.18), residues: 1950 helix: -0.13 (0.16), residues: 1063 sheet: 0.40 (0.31), residues: 277 loop : 0.19 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 179 TYR 0.027 0.001 TYR C 124 PHE 0.009 0.001 PHE D 70 HIS 0.008 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00428 (16607) covalent geometry : angle 0.64675 (22614) hydrogen bonds : bond 0.07185 ( 793) hydrogen bonds : angle 5.73281 ( 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 288 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 275 time to evaluate : 0.897 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 68 MET cc_start: 0.9211 (tpp) cc_final: 0.8839 (tpp) REVERT: A 76 MET cc_start: 0.9050 (mmm) cc_final: 0.8771 (mmt) REVERT: A 79 ASN cc_start: 0.8421 (m-40) cc_final: 0.7857 (m-40) REVERT: A 178 MET cc_start: 0.9246 (mmm) cc_final: 0.8995 (mmt) REVERT: A 199 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7700 (mmt) REVERT: A 222 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.7888 (ttm170) REVERT: A 309 MET cc_start: 0.8187 (ttm) cc_final: 0.7923 (ttp) REVERT: C 110 ASP cc_start: 0.8669 (t0) cc_final: 0.8431 (m-30) REVERT: C 121 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 178 MET cc_start: 0.9276 (mmt) cc_final: 0.8784 (mmt) REVERT: D 39 LYS cc_start: 0.8190 (tttt) cc_final: 0.7956 (tptp) REVERT: E 81 LYS cc_start: 0.8442 (mttt) cc_final: 0.7751 (tptt) REVERT: E 105 ASP cc_start: 0.7938 (m-30) cc_final: 0.7638 (m-30) REVERT: E 127 MET cc_start: 0.8090 (mtp) cc_final: 0.7748 (mtm) REVERT: E 272 MET cc_start: 0.8187 (mtt) cc_final: 0.7947 (mtt) REVERT: E 325 MET cc_start: 0.7274 (mmm) cc_final: 0.7035 (mmp) REVERT: E 330 THR cc_start: 0.8024 (m) cc_final: 0.7727 (p) REVERT: F 100 ASP cc_start: 0.8174 (t0) cc_final: 0.7959 (t0) REVERT: F 102 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7888 (mm-30) REVERT: F 252 ASP cc_start: 0.7943 (m-30) cc_final: 0.7400 (p0) REVERT: H 200 ARG cc_start: 0.8111 (ttt180) cc_final: 0.7617 (mtp-110) outliers start: 13 outliers final: 10 residues processed: 282 average time/residue: 0.3438 time to fit residues: 135.5335 Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 249 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 199 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 88 ILE 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 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: 3.9990 chunk 179 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 181 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.099984 restraints weight = 66485.737| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.23 r_work: 0.3011 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16607 Z= 0.151 Angle : 0.565 6.124 22614 Z= 0.301 Chirality : 0.040 0.170 2554 Planarity : 0.005 0.044 2808 Dihedral : 14.402 143.708 2599 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.98 % Allowed : 7.56 % 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: 0.26 (0.19), residues: 1950 helix: 0.30 (0.16), residues: 1069 sheet: 0.30 (0.30), residues: 275 loop : 0.20 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 143 TYR 0.023 0.001 TYR C 124 PHE 0.007 0.001 PHE D 70 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00340 (16607) covalent geometry : angle 0.56454 (22614) hydrogen bonds : bond 0.06006 ( 793) hydrogen bonds : angle 5.20565 ( 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 277 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 261 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8941 (mmm) cc_final: 0.8731 (mmt) REVERT: A 79 ASN cc_start: 0.8392 (m-40) cc_final: 0.7835 (m-40) REVERT: A 178 MET cc_start: 0.9240 (mmm) cc_final: 0.8986 (mmt) REVERT: A 222 ARG cc_start: 0.8244 (ttp-170) cc_final: 0.7899 (ttm170) REVERT: A 309 MET cc_start: 0.8212 (ttm) cc_final: 0.7963 (ttp) REVERT: C 110 ASP cc_start: 0.8648 (t0) cc_final: 0.8406 (m-30) REVERT: C 121 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7829 (mt-10) REVERT: C 147 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7466 (mp) REVERT: C 178 MET cc_start: 0.9273 (mmt) cc_final: 0.8851 (mmt) REVERT: E 81 LYS cc_start: 0.8426 (mttt) cc_final: 0.7775 (tptt) REVERT: E 272 MET cc_start: 0.8061 (mtt) cc_final: 0.7834 (mtt) REVERT: E 328 ASP cc_start: 0.7948 (t0) cc_final: 0.7651 (m-30) REVERT: E 330 THR cc_start: 0.8011 (m) cc_final: 0.7712 (p) REVERT: F 84 SER cc_start: 0.8804 (p) cc_final: 0.8570 (t) REVERT: F 102 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7905 (mm-30) REVERT: H 200 ARG cc_start: 0.8073 (ttt180) cc_final: 0.7555 (mtp-110) outliers start: 16 outliers final: 10 residues processed: 269 average time/residue: 0.3445 time to fit residues: 129.5206 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 : 0.672 ------------------------------------------------------------------------------- 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 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 125 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 178 optimal weight: 0.4980 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: 0.9990 chunk 166 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.099177 restraints weight = 66535.186| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.23 r_work: 0.2926 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3063 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= 0.149 Angle : 0.540 6.234 22614 Z= 0.285 Chirality : 0.040 0.137 2554 Planarity : 0.005 0.043 2808 Dihedral : 14.325 147.235 2599 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.28 % Allowed : 7.56 % Favored : 91.16 % 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: 0.49 (0.19), residues: 1950 helix: 0.58 (0.16), residues: 1070 sheet: 0.31 (0.30), residues: 281 loop : 0.16 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 291 TYR 0.022 0.001 TYR C 124 PHE 0.007 0.001 PHE C 25 HIS 0.009 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00343 (16607) covalent geometry : angle 0.54036 (22614) hydrogen bonds : bond 0.05138 ( 793) hydrogen bonds : angle 4.86762 ( 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 271 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.875 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: 0.8866 (mmm) cc_final: 0.8665 (mmt) REVERT: A 79 ASN cc_start: 0.8386 (m-40) cc_final: 0.7828 (m-40) REVERT: A 178 MET cc_start: 0.9238 (mmm) cc_final: 0.9007 (mmt) REVERT: A 222 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7855 (ttm170) REVERT: A 309 MET cc_start: 0.8221 (ttm) cc_final: 0.7915 (ttp) REVERT: C 110 ASP cc_start: 0.8724 (t0) cc_final: 0.8438 (m-30) REVERT: C 121 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7861 (mt-10) REVERT: C 147 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7414 (mp) REVERT: C 178 MET cc_start: 0.9266 (mmt) cc_final: 0.8745 (mmt) REVERT: E 81 LYS cc_start: 0.8425 (mttt) cc_final: 0.7724 (tptt) REVERT: E 135 MET cc_start: 0.7432 (ttm) cc_final: 0.7099 (ttm) REVERT: E 272 MET cc_start: 0.8136 (mtt) cc_final: 0.7911 (mtt) REVERT: E 330 THR cc_start: 0.8118 (m) cc_final: 0.7796 (p) REVERT: F 102 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7853 (mm-30) REVERT: H 200 ARG cc_start: 0.8075 (ttt180) cc_final: 0.7556 (mtp-110) outliers start: 21 outliers final: 12 residues processed: 258 average time/residue: 0.3453 time to fit residues: 125.0302 Evaluate side-chains 253 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 188 GLU 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: 0.5980 chunk 100 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.100789 restraints weight = 66112.418| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.21 r_work: 0.3019 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16607 Z= 0.122 Angle : 0.518 6.253 22614 Z= 0.271 Chirality : 0.039 0.132 2554 Planarity : 0.004 0.066 2808 Dihedral : 14.200 146.748 2599 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.10 % Allowed : 8.23 % Favored : 90.68 % 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: 0.69 (0.19), residues: 1950 helix: 0.80 (0.16), residues: 1069 sheet: 0.20 (0.30), residues: 271 loop : 0.23 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 169 TYR 0.020 0.001 TYR C 124 PHE 0.006 0.001 PHE A 58 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00275 (16607) covalent geometry : angle 0.51809 (22614) hydrogen bonds : bond 0.04557 ( 793) hydrogen bonds : angle 4.67171 ( 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 268 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.864 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 79 ASN cc_start: 0.8365 (m-40) cc_final: 0.7815 (m-40) REVERT: A 178 MET cc_start: 0.9239 (mmm) cc_final: 0.8999 (mmt) REVERT: A 222 ARG cc_start: 0.8279 (ttp-170) cc_final: 0.7943 (ttm170) REVERT: A 286 ASN cc_start: 0.7795 (m110) cc_final: 0.7535 (m110) REVERT: A 309 MET cc_start: 0.8246 (ttm) cc_final: 0.7978 (ttp) REVERT: C 110 ASP cc_start: 0.8631 (t0) cc_final: 0.8364 (m-30) REVERT: C 147 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7515 (mp) REVERT: C 178 MET cc_start: 0.9251 (mmt) cc_final: 0.8872 (mmt) REVERT: D 120 GLU cc_start: 0.7602 (tt0) cc_final: 0.7092 (tt0) REVERT: D 135 MET cc_start: 0.7698 (mmm) cc_final: 0.7418 (mmt) REVERT: E 81 LYS cc_start: 0.8527 (mttt) cc_final: 0.7768 (tptt) REVERT: E 135 MET cc_start: 0.7419 (ttm) cc_final: 0.7079 (ttm) REVERT: E 272 MET cc_start: 0.8063 (mtt) cc_final: 0.7842 (mtt) REVERT: E 328 ASP cc_start: 0.7925 (t0) cc_final: 0.7687 (m-30) REVERT: E 330 THR cc_start: 0.8107 (m) cc_final: 0.7795 (p) REVERT: F 102 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7877 (mm-30) REVERT: H 200 ARG cc_start: 0.8030 (ttt180) cc_final: 0.7575 (mtp-110) outliers start: 18 outliers final: 13 residues processed: 257 average time/residue: 0.3487 time to fit residues: 125.9866 Evaluate side-chains 256 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 242 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 B residue 128 GLU 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 144 SER Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 240 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 4 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.100192 restraints weight = 66427.897| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.16 r_work: 0.3000 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3339 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= 0.132 Angle : 0.515 6.278 22614 Z= 0.269 Chirality : 0.039 0.124 2554 Planarity : 0.004 0.057 2808 Dihedral : 14.112 146.561 2599 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.98 % Allowed : 8.96 % Favored : 90.07 % 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: 0.80 (0.19), residues: 1950 helix: 0.92 (0.16), residues: 1072 sheet: 0.20 (0.30), residues: 271 loop : 0.24 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 covalent geometry : bond 0.00307 (16607) covalent geometry : angle 0.51546 (22614) hydrogen bonds : bond 0.04451 ( 793) hydrogen bonds : angle 4.56892 ( 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 262 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 0.896 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: 0.8282 (m-40) cc_final: 0.7717 (m-40) REVERT: A 178 MET cc_start: 0.9271 (mmm) cc_final: 0.9024 (mmt) REVERT: A 222 ARG cc_start: 0.8261 (ttp-170) cc_final: 0.7931 (ttm170) REVERT: A 286 ASN cc_start: 0.7747 (m110) cc_final: 0.7462 (m110) REVERT: A 309 MET cc_start: 0.8229 (ttm) cc_final: 0.7959 (ttp) REVERT: C 110 ASP cc_start: 0.8624 (t0) cc_final: 0.8347 (m-30) REVERT: C 147 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7515 (mp) REVERT: C 178 MET cc_start: 0.9236 (mmt) cc_final: 0.8835 (mmt) REVERT: C 290 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7519 (mt-10) REVERT: D 39 LYS cc_start: 0.8146 (tttt) cc_final: 0.7867 (tptp) REVERT: D 135 MET cc_start: 0.7502 (mmm) cc_final: 0.7211 (mmt) REVERT: E 81 LYS cc_start: 0.8515 (mttt) cc_final: 0.7818 (tptt) REVERT: E 135 MET cc_start: 0.7343 (ttm) cc_final: 0.6992 (ttm) REVERT: E 272 MET cc_start: 0.8132 (mtt) cc_final: 0.7922 (mtt) REVERT: E 330 THR cc_start: 0.8144 (m) cc_final: 0.7854 (p) REVERT: F 102 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7867 (mm-30) REVERT: H 200 ARG cc_start: 0.8087 (ttt180) cc_final: 0.7618 (mtp-110) outliers start: 16 outliers final: 14 residues processed: 253 average time/residue: 0.3568 time to fit residues: 125.5599 Evaluate side-chains 250 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 D residue 83 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain F residue 240 ASP 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: 0.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 chunk 81 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100661 restraints weight = 66484.291| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.15 r_work: 0.3028 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3474 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= 0.119 Angle : 0.511 6.250 22614 Z= 0.264 Chirality : 0.039 0.125 2554 Planarity : 0.004 0.064 2808 Dihedral : 14.033 146.986 2599 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.91 % Allowed : 9.38 % Favored : 89.70 % 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: 0.97 (0.19), residues: 1950 helix: 1.08 (0.16), residues: 1073 sheet: 0.19 (0.30), residues: 271 loop : 0.31 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 160 TYR 0.018 0.001 TYR C 124 PHE 0.006 0.001 PHE A 58 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00274 (16607) covalent geometry : angle 0.51067 (22614) hydrogen bonds : bond 0.04177 ( 793) hydrogen bonds : angle 4.45519 ( 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 257 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 0.836 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: 0.8268 (m-40) cc_final: 0.7699 (m-40) REVERT: A 178 MET cc_start: 0.9262 (mmm) cc_final: 0.9020 (mmt) REVERT: A 222 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7931 (ttm170) REVERT: A 309 MET cc_start: 0.8247 (ttm) cc_final: 0.7974 (ttp) REVERT: C 90 LYS cc_start: 0.8207 (pttt) cc_final: 0.7961 (mtmm) REVERT: C 135 MET cc_start: 0.3969 (mmm) cc_final: 0.3760 (mmm) REVERT: C 147 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7550 (mp) REVERT: C 178 MET cc_start: 0.9217 (mmt) cc_final: 0.8815 (mmt) REVERT: D 39 LYS cc_start: 0.8168 (tttt) cc_final: 0.7877 (tptp) REVERT: D 110 ASP cc_start: 0.8376 (t0) cc_final: 0.8046 (t0) REVERT: D 135 MET cc_start: 0.7639 (mmm) cc_final: 0.7331 (mmt) REVERT: E 81 LYS cc_start: 0.8526 (mttt) cc_final: 0.7815 (tptt) REVERT: E 117 MET cc_start: 0.7317 (tpp) cc_final: 0.7047 (tpt) REVERT: E 135 MET cc_start: 0.7354 (ttm) cc_final: 0.7044 (ttm) REVERT: E 330 THR cc_start: 0.8139 (m) cc_final: 0.7831 (p) REVERT: F 102 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7866 (mm-30) REVERT: H 200 ARG cc_start: 0.8062 (ttt180) cc_final: 0.7593 (mtp-110) outliers start: 15 outliers final: 11 residues processed: 248 average time/residue: 0.3521 time to fit residues: 122.0008 Evaluate side-chains 252 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 D residue 83 THR Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 240 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 166 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 160 optimal weight: 0.0060 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099419 restraints weight = 66856.595| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.16 r_work: 0.3035 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3536 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= 0.129 Angle : 0.512 6.222 22614 Z= 0.266 Chirality : 0.039 0.124 2554 Planarity : 0.004 0.063 2808 Dihedral : 14.006 146.437 2599 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.10 % Allowed : 9.51 % Favored : 89.40 % 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: 1.06 (0.19), residues: 1950 helix: 1.14 (0.16), residues: 1074 sheet: 0.27 (0.30), residues: 281 loop : 0.37 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 160 TYR 0.019 0.001 TYR C 124 PHE 0.006 0.001 PHE A 58 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00300 (16607) covalent geometry : angle 0.51183 (22614) hydrogen bonds : bond 0.04252 ( 793) hydrogen bonds : angle 4.42487 ( 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 259 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.758 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 79 ASN cc_start: 0.8278 (m-40) cc_final: 0.7721 (m-40) REVERT: A 178 MET cc_start: 0.9277 (mmm) cc_final: 0.9050 (mmt) REVERT: A 222 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7928 (ttm170) REVERT: A 286 ASN cc_start: 0.7748 (m110) cc_final: 0.7438 (m110) REVERT: A 309 MET cc_start: 0.8267 (ttm) cc_final: 0.7996 (ttp) REVERT: C 90 LYS cc_start: 0.8224 (pttt) cc_final: 0.7973 (mtmm) REVERT: C 147 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7558 (mp) REVERT: C 178 MET cc_start: 0.9219 (mmt) cc_final: 0.8824 (mmt) REVERT: D 39 LYS cc_start: 0.8145 (tttt) cc_final: 0.7863 (tptp) REVERT: D 135 MET cc_start: 0.7654 (mmm) cc_final: 0.7351 (mmt) REVERT: E 81 LYS cc_start: 0.8404 (mttt) cc_final: 0.7759 (tptt) REVERT: E 105 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: E 117 MET cc_start: 0.7237 (tpp) cc_final: 0.6989 (tpt) REVERT: E 135 MET cc_start: 0.7371 (ttm) cc_final: 0.7028 (ttm) REVERT: E 330 THR cc_start: 0.8145 (m) cc_final: 0.7850 (p) REVERT: F 102 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7866 (mm-30) REVERT: H 200 ARG cc_start: 0.8070 (ttt180) cc_final: 0.7589 (mtp-110) outliers start: 18 outliers final: 14 residues processed: 248 average time/residue: 0.3452 time to fit residues: 119.8962 Evaluate side-chains 257 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 D residue 83 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 291 ARG 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: 0.9980 chunk 50 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 74 optimal weight: 0.0000 chunk 47 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.100857 restraints weight = 65962.443| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.14 r_work: 0.3009 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.003 0.041 16607 Z= 0.113 Angle : 0.511 6.252 22614 Z= 0.265 Chirality : 0.039 0.125 2554 Planarity : 0.004 0.062 2808 Dihedral : 13.968 146.937 2599 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.98 % Allowed : 9.93 % Favored : 89.09 % 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: 1.17 (0.19), residues: 1950 helix: 1.23 (0.16), residues: 1074 sheet: 0.28 (0.29), residues: 280 loop : 0.42 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 160 TYR 0.018 0.001 TYR C 124 PHE 0.006 0.001 PHE A 58 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00257 (16607) covalent geometry : angle 0.51147 (22614) hydrogen bonds : bond 0.04004 ( 793) hydrogen bonds : angle 4.36680 ( 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: 16 poor density : 245 time to evaluate : 0.875 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 79 ASN cc_start: 0.8269 (m-40) cc_final: 0.7702 (m-40) REVERT: A 178 MET cc_start: 0.9265 (mmm) cc_final: 0.9044 (mmt) REVERT: A 222 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7931 (ttm170) REVERT: A 286 ASN cc_start: 0.7801 (m110) cc_final: 0.7484 (m110) REVERT: A 309 MET cc_start: 0.8248 (ttm) cc_final: 0.7982 (ttp) REVERT: B 105 ASP cc_start: 0.8837 (m-30) cc_final: 0.8594 (t0) REVERT: C 90 LYS cc_start: 0.8212 (pttt) cc_final: 0.7972 (mtmm) REVERT: C 147 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7551 (mp) REVERT: C 178 MET cc_start: 0.9226 (mmt) cc_final: 0.8835 (mmt) REVERT: D 39 LYS cc_start: 0.8137 (tttt) cc_final: 0.7862 (tptp) REVERT: D 135 MET cc_start: 0.7738 (mmm) cc_final: 0.7431 (mmt) REVERT: E 81 LYS cc_start: 0.8386 (mttt) cc_final: 0.7737 (tptt) REVERT: E 105 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: E 117 MET cc_start: 0.7221 (tpp) cc_final: 0.6980 (tpt) REVERT: E 135 MET cc_start: 0.7346 (ttm) cc_final: 0.7012 (ttm) REVERT: E 330 THR cc_start: 0.8147 (m) cc_final: 0.7860 (p) REVERT: F 102 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7854 (mm-30) REVERT: F 296 ASP cc_start: 0.7755 (m-30) cc_final: 0.7503 (m-30) REVERT: H 200 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7587 (mtp-110) outliers start: 16 outliers final: 12 residues processed: 251 average time/residue: 0.3385 time to fit residues: 119.4202 Evaluate side-chains 252 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 163 MET 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 105 ASP Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 291 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 27 optimal weight: 0.0970 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.100150 restraints weight = 66479.125| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.15 r_work: 0.3040 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16607 Z= 0.126 Angle : 0.518 6.291 22614 Z= 0.268 Chirality : 0.039 0.133 2554 Planarity : 0.004 0.066 2808 Dihedral : 13.940 146.439 2599 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.85 % Allowed : 10.48 % Favored : 88.67 % 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: 1.19 (0.19), residues: 1950 helix: 1.28 (0.16), residues: 1076 sheet: 0.26 (0.29), residues: 282 loop : 0.39 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 169 TYR 0.018 0.001 TYR C 124 PHE 0.006 0.001 PHE C 25 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00294 (16607) covalent geometry : angle 0.51779 (22614) hydrogen bonds : bond 0.04097 ( 793) hydrogen bonds : angle 4.35293 ( 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 257 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.746 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: 0.8244 (m-40) cc_final: 0.7686 (m-40) REVERT: A 178 MET cc_start: 0.9275 (mmm) cc_final: 0.9062 (mmt) REVERT: A 222 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7943 (ttm170) REVERT: A 309 MET cc_start: 0.8322 (ttm) cc_final: 0.8043 (ttp) REVERT: B 105 ASP cc_start: 0.8841 (m-30) cc_final: 0.8598 (t0) REVERT: C 90 LYS cc_start: 0.8152 (pttt) cc_final: 0.7896 (mtmm) REVERT: C 110 ASP cc_start: 0.8663 (t0) cc_final: 0.8378 (m-30) REVERT: C 147 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7449 (mp) REVERT: C 178 MET cc_start: 0.9245 (mmt) cc_final: 0.8854 (mmt) REVERT: D 39 LYS cc_start: 0.8151 (tttt) cc_final: 0.7842 (tptp) REVERT: E 81 LYS cc_start: 0.8320 (mttt) cc_final: 0.7756 (tptt) REVERT: E 117 MET cc_start: 0.7230 (tpp) cc_final: 0.6998 (tpt) REVERT: E 135 MET cc_start: 0.7338 (ttm) cc_final: 0.7009 (ttm) REVERT: E 330 THR cc_start: 0.8112 (m) cc_final: 0.7825 (p) REVERT: F 102 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7861 (mm-30) REVERT: F 296 ASP cc_start: 0.7899 (m-30) cc_final: 0.7695 (m-30) REVERT: H 200 ARG cc_start: 0.7995 (ttt180) cc_final: 0.7595 (mtp-110) outliers start: 14 outliers final: 13 residues processed: 247 average time/residue: 0.3400 time to fit residues: 117.6789 Evaluate side-chains 253 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 239 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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 D residue 83 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 240 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 26 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 131 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.100086 restraints weight = 66191.348| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.14 r_work: 0.2992 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16607 Z= 0.128 Angle : 0.517 6.303 22614 Z= 0.267 Chirality : 0.039 0.129 2554 Planarity : 0.005 0.092 2808 Dihedral : 13.928 146.440 2599 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.98 % Allowed : 10.54 % Favored : 88.48 % 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: 1.23 (0.19), residues: 1950 helix: 1.32 (0.16), residues: 1076 sheet: 0.25 (0.29), residues: 282 loop : 0.39 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 169 TYR 0.018 0.001 TYR C 124 PHE 0.006 0.001 PHE C 152 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00299 (16607) covalent geometry : angle 0.51728 (22614) hydrogen bonds : bond 0.04112 ( 793) hydrogen bonds : angle 4.33801 ( 2241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7651.90 seconds wall clock time: 130 minutes 7.49 seconds (7807.49 seconds total)