Starting phenix.real_space_refine on Mon Jul 6 02:37:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbn_13296/07_2026/7pbn_13296_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbn_13296/07_2026/7pbn_13296.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/7pbn_13296/07_2026/7pbn_13296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbn_13296/07_2026/7pbn_13296.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbn_13296/07_2026/7pbn_13296_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbn_13296/07_2026/7pbn_13296_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 44 5.49 5 Mg 3 5.21 5 S 100 5.16 5 C 10134 2.51 5 N 2757 2.21 5 O 3218 1.98 5 H 15818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32074 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: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 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: 4.84, per 1000 atoms: 0.15 Number of scatterers: 32074 At special positions: 0 Unit cell: (125.35, 138.43, 109, 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 100 16.00 P 44 15.00 Mg 3 11.99 O 3218 8.00 N 2757 7.00 C 10134 6.00 H 15818 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: 2.14 Conformation dependent library (CDL) restraints added in 792.0 milliseconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 20 sheets defined 60.3% alpha, 10.9% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.517A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.760A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.541A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 removed outlier: 3.635A pdb=" N MET A 115 " --> pdb=" O ILE A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.886A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.676A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.661A pdb=" N GLU A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.874A 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 ILE A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 removed outlier: 3.540A pdb=" N VAL A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.659A pdb=" N GLU A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.746A pdb=" N LEU A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.603A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.523A 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: 4.611A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 128 " --> pdb=" O TYR B 124 " (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 removed outlier: 3.600A pdb=" N GLU B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 removed outlier: 3.615A pdb=" N GLU B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 removed outlier: 3.508A pdb=" N TYR B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.652A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'C' and resid 31 through 48 Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.770A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.723A 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: 3.984A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.654A 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 172 removed outlier: 3.535A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.570A pdb=" N ILE C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.558A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 235 removed outlier: 3.663A pdb=" N ILE C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.749A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 273 removed outlier: 3.521A 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 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.843A 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 31 through 47 removed outlier: 3.611A 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 100 removed outlier: 3.736A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 130 removed outlier: 4.438A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.634A 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 160 through 164 Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.586A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.180A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.631A pdb=" N GLU D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 232 Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.556A pdb=" N GLY D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 removed outlier: 3.589A 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: 3.638A 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: 3.621A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.748A 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: 3.543A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.769A pdb=" N MET E 115 " --> pdb=" O ILE E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 115' Processing helix chain 'E' and resid 116 through 130 removed outlier: 4.489A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.684A 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: 3.710A pdb=" N GLU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 213 Processing helix chain 'E' and resid 216 through 235 removed outlier: 3.634A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 removed outlier: 3.551A 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: 3.591A pdb=" N ASP E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.902A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.520A 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: 3.649A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.731A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.505A 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 160 through 164 Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 removed outlier: 3.671A pdb=" N GLU F 188 " --> pdb=" O PRO F 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.874A pdb=" N GLU F 271 " --> pdb=" O ARG F 267 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.596A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 318 through 326 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: 3.744A 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: 3.686A pdb=" N ASP A 110 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.886A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 removed outlier: 7.029A 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: 6.552A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.985A 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: 6.258A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.660A 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: 3.580A pdb=" N ASP D 110 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (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: 6.608A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.796A 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: 7.027A 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: 6.245A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.789A 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 Processing sheet with id=AC2, first strand: chain 'F' and resid 308 through 311 779 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 6.22 Time building geometry restraints manager: 2.94 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: 15818 1.06 - 1.28: 2721 1.28 - 1.50: 6867 1.50 - 1.72: 6817 1.72 - 1.94: 198 Bond restraints: 32421 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 C 19 " pdb=" H1 THR C 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 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 ASP H 158 " pdb=" H1 ASP H 158 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+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 2.49e+01 ... (remaining 32416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 57940 2.01 - 4.02: 652 4.02 - 6.03: 68 6.03 - 8.04: 9 8.04 - 10.06: 15 Bond angle restraints: 58684 Sorted by residual: angle pdb=" C4' DC V 8 " pdb=" O4' DC V 8 " pdb=" C1' DC V 8 " ideal model delta sigma weight residual 110.10 105.14 4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.24e+01 angle pdb=" C4' DT V 15 " pdb=" O4' DT V 15 " pdb=" C1' DT V 15 " ideal model delta sigma weight residual 110.10 105.93 4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" O4' DA U 13 " pdb=" C1' DA U 13 " pdb=" N9 DA U 13 " ideal model delta sigma weight residual 108.00 110.88 -2.88 7.00e-01 2.04e+00 1.70e+01 angle pdb=" N3 DT V 3 " pdb=" C4 DT V 3 " pdb=" O4 DT V 3 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 58679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.28: 14431 31.28 - 62.57: 590 62.57 - 93.85: 40 93.85 - 125.14: 1 125.14 - 156.42: 4 Dihedral angle restraints: 15066 sinusoidal: 8633 harmonic: 6433 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 96.42 -156.42 1 2.00e+01 2.50e-03 4.60e+01 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 91.76 -151.76 1 2.00e+01 2.50e-03 4.51e+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 79.17 -139.17 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 15063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2264 0.072 - 0.143: 266 0.143 - 0.215: 15 0.215 - 0.287: 2 0.287 - 0.358: 1 Chirality restraints: 2548 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.69 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C3' AGS B 401 " pdb=" C2' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" O3' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2545 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 218 " 0.037 9.50e-02 1.11e+02 5.02e-02 5.34e+01 pdb=" NE ARG F 218 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG F 218 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG F 218 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 218 " -0.093 2.00e-02 2.50e+03 pdb="HH11 ARG F 218 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 218 " -0.007 2.00e-02 2.50e+03 pdb="HH21 ARG F 218 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARG F 218 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 192 " 0.100 9.50e-02 1.11e+02 5.50e-02 4.40e+01 pdb=" NE ARG A 192 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG A 192 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 192 " 0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG A 192 " -0.074 2.00e-02 2.50e+03 pdb="HH11 ARG A 192 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 192 " -0.058 2.00e-02 2.50e+03 pdb="HH21 ARG A 192 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 192 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.039 2.00e-02 2.50e+03 4.82e-02 3.49e+01 pdb=" CD GLN C 31 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.077 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.002 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.074 2.00e-02 2.50e+03 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 693 2.13 - 2.75: 56276 2.75 - 3.36: 84673 3.36 - 3.98: 107981 3.98 - 4.60: 175389 Nonbonded interactions: 425012 Sorted by model distance: nonbonded pdb=" HG1 THR F 311 " pdb=" O GLY F 314 " model vdw 1.509 2.450 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.558 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.580 2.450 nonbonded pdb=" HZ3 LYS E 81 " pdb=" O ASP E 100 " model vdw 1.582 2.450 nonbonded pdb=" HG1 THR F 66 " pdb=" O1B ADP F 600 " model vdw 1.590 2.450 ... (remaining 425007 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.110 Find NCS groups from input model: 0.650 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 0.098 16603 Z= 0.246 Angle : 0.776 10.056 22607 Z= 0.452 Chirality : 0.046 0.358 2548 Planarity : 0.010 0.153 2808 Dihedral : 15.085 156.423 6439 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.06 % Allowed : 1.40 % Favored : 98.54 % 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: -0.88 (0.18), residues: 1950 helix: -1.20 (0.14), residues: 1039 sheet: 0.50 (0.29), residues: 304 loop : 0.46 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.004 ARG F 212 TYR 0.039 0.005 TYR D 131 PHE 0.020 0.003 PHE C 25 HIS 0.010 0.003 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.25 (16603) covalent geometry : angle 0.77617 / 0.45 (22607) hydrogen bonds : bond 0.25940 / 17.29 ( 807) hydrogen bonds : angle 8.43706 / 5.95 ( 2273) *********************** 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 416 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8566 (tpp) cc_final: 0.8357 (tpp) REVERT: A 76 MET cc_start: 0.9093 (mmm) cc_final: 0.8778 (mmt) REVERT: A 105 ASP cc_start: 0.7834 (m-30) cc_final: 0.7607 (m-30) REVERT: A 296 ASP cc_start: 0.7518 (m-30) cc_final: 0.7305 (m-30) REVERT: B 295 GLU cc_start: 0.8089 (tt0) cc_final: 0.7830 (tt0) REVERT: C 90 LYS cc_start: 0.8236 (pttt) cc_final: 0.7951 (pttm) REVERT: C 178 MET cc_start: 0.9169 (mmt) cc_final: 0.7933 (mmt) REVERT: C 291 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7979 (ttm170) REVERT: D 68 MET cc_start: 0.9164 (tpt) cc_final: 0.8559 (tpt) REVERT: D 171 ARG cc_start: 0.8409 (mmt-90) cc_final: 0.8070 (mpt90) REVERT: D 309 MET cc_start: 0.8894 (mtp) cc_final: 0.8598 (mtp) REVERT: E 178 MET cc_start: 0.9253 (mmm) cc_final: 0.9024 (mmt) REVERT: E 256 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7565 (mm-30) REVERT: E 272 MET cc_start: 0.8013 (mtt) cc_final: 0.7751 (mtt) REVERT: F 117 MET cc_start: 0.7951 (tpt) cc_final: 0.7527 (tpt) REVERT: F 213 SER cc_start: 0.8588 (t) cc_final: 0.8355 (p) REVERT: G 164 VAL cc_start: 0.8569 (t) cc_final: 0.8252 (p) REVERT: G 180 MET cc_start: 0.6892 (mtp) cc_final: 0.6612 (mtm) REVERT: G 203 LEU cc_start: 0.7626 (tp) cc_final: 0.6585 (tp) REVERT: H 194 LEU cc_start: 0.8917 (mt) cc_final: 0.8670 (mt) outliers start: 1 outliers final: 1 residues processed: 416 average time/residue: 0.3584 time to fit residues: 201.8413 Evaluate side-chains 262 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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: 0.5980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN C 99 ASN D 166 ASN D 246 GLN F 255 HIS H 161 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.090049 restraints weight = 70134.981| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.32 r_work: 0.2889 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 0.036 16603 Z= 0.178 Angle : 0.669 6.722 22607 Z= 0.362 Chirality : 0.043 0.167 2548 Planarity : 0.006 0.056 2808 Dihedral : 14.666 146.033 2626 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.91 % Allowed : 6.40 % 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: 0.04 (0.18), residues: 1950 helix: -0.11 (0.15), residues: 1079 sheet: 1.09 (0.31), residues: 271 loop : 0.14 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 267 TYR 0.020 0.001 TYR C 124 PHE 0.008 0.001 PHE C 108 HIS 0.008 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (16603) covalent geometry : angle 0.66875 / 0.36 (22607) hydrogen bonds : bond 0.08084 / 5.34 ( 807) hydrogen bonds : angle 6.03947 / 4.22 ( 2273) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 270 time to evaluate : 0.834 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: A 76 MET cc_start: 0.9379 (mmm) cc_final: 0.9149 (mmt) REVERT: A 163 MET cc_start: 0.8948 (mmm) cc_final: 0.8695 (mmp) REVERT: A 291 ARG cc_start: 0.8057 (tpt-90) cc_final: 0.7817 (tpt-90) REVERT: A 296 ASP cc_start: 0.8109 (m-30) cc_final: 0.7867 (m-30) REVERT: B 295 GLU cc_start: 0.8744 (tt0) cc_final: 0.8484 (tt0) REVERT: C 90 LYS cc_start: 0.8179 (pttt) cc_final: 0.7889 (pttm) REVERT: C 105 ASP cc_start: 0.8460 (m-30) cc_final: 0.8238 (m-30) REVERT: C 325 MET cc_start: 0.9049 (mmp) cc_final: 0.8807 (mmp) REVERT: D 68 MET cc_start: 0.9367 (tpt) cc_final: 0.8829 (tpt) REVERT: D 171 ARG cc_start: 0.8712 (mmt-90) cc_final: 0.8403 (mpt90) REVERT: D 309 MET cc_start: 0.9046 (mtp) cc_final: 0.8770 (mtp) REVERT: E 254 ASP cc_start: 0.8769 (t0) cc_final: 0.8565 (t0) REVERT: E 256 GLU cc_start: 0.8612 (mm-30) cc_final: 0.7961 (mm-30) REVERT: E 272 MET cc_start: 0.8417 (mtt) cc_final: 0.8082 (mtt) REVERT: F 213 SER cc_start: 0.8851 (t) cc_final: 0.8616 (p) REVERT: F 295 GLU cc_start: 0.8434 (tt0) cc_final: 0.7897 (tt0) REVERT: G 160 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7301 (tm-30) REVERT: G 203 LEU cc_start: 0.7105 (tp) cc_final: 0.6900 (tp) outliers start: 15 outliers final: 13 residues processed: 276 average time/residue: 0.3020 time to fit residues: 119.1241 Evaluate side-chains 273 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 287 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 324 HIS C 99 ASN D 166 ASN D 286 ASN F 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.090141 restraints weight = 69800.545| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.28 r_work: 0.2879 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16603 Z= 0.153 Angle : 0.594 8.687 22607 Z= 0.312 Chirality : 0.041 0.183 2548 Planarity : 0.005 0.051 2808 Dihedral : 14.330 137.380 2626 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.16 % Allowed : 7.37 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1950 helix: 0.22 (0.16), residues: 1087 sheet: 0.93 (0.31), residues: 262 loop : 0.14 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 267 TYR 0.018 0.001 TYR C 124 PHE 0.008 0.001 PHE B 58 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (16603) covalent geometry : angle 0.59360 / 0.31 (22607) hydrogen bonds : bond 0.06405 / 4.19 ( 807) hydrogen bonds : angle 5.33254 / 3.74 ( 2273) *********************** 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 280 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.9312 (mmm) cc_final: 0.9062 (mmt) REVERT: A 163 MET cc_start: 0.8962 (mmm) cc_final: 0.8760 (mmt) REVERT: A 291 ARG cc_start: 0.8016 (tpt-90) cc_final: 0.7747 (tpt-90) REVERT: A 296 ASP cc_start: 0.8031 (m-30) cc_final: 0.7795 (m-30) REVERT: B 242 LYS cc_start: 0.8818 (tppp) cc_final: 0.8454 (mmtt) REVERT: B 295 GLU cc_start: 0.8709 (tt0) cc_final: 0.8460 (tt0) REVERT: C 90 LYS cc_start: 0.8110 (pttt) cc_final: 0.7824 (pttm) REVERT: C 105 ASP cc_start: 0.8458 (m-30) cc_final: 0.8248 (m-30) REVERT: C 135 MET cc_start: 0.4514 (mmm) cc_final: 0.4061 (mmm) REVERT: C 325 MET cc_start: 0.9001 (mmp) cc_final: 0.8693 (mmp) REVERT: D 171 ARG cc_start: 0.8696 (mmt-90) cc_final: 0.8373 (mpt90) REVERT: D 309 MET cc_start: 0.9046 (mtp) cc_final: 0.8774 (mtp) REVERT: E 256 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8303 (mm-30) REVERT: E 272 MET cc_start: 0.8382 (mtt) cc_final: 0.8054 (mtt) REVERT: F 211 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8424 (ttp-110) REVERT: F 213 SER cc_start: 0.8896 (t) cc_final: 0.8670 (p) REVERT: F 295 GLU cc_start: 0.8468 (tt0) cc_final: 0.8008 (tt0) REVERT: F 310 ARG cc_start: 0.7463 (mtm180) cc_final: 0.7218 (ttp80) REVERT: G 160 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7778 (tm-30) REVERT: G 161 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7990 (mm-40) REVERT: G 192 GLU cc_start: 0.7640 (tt0) cc_final: 0.7348 (mp0) REVERT: G 203 LEU cc_start: 0.6926 (tp) cc_final: 0.6697 (tp) outliers start: 19 outliers final: 13 residues processed: 272 average time/residue: 0.3500 time to fit residues: 135.1540 Evaluate side-chains 264 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 250 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 287 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 185 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.090655 restraints weight = 69824.100| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.25 r_work: 0.2891 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16603 Z= 0.134 Angle : 0.562 7.474 22607 Z= 0.291 Chirality : 0.040 0.180 2548 Planarity : 0.004 0.044 2808 Dihedral : 14.109 131.433 2626 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.28 % Allowed : 7.74 % Favored : 90.98 % 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: 0.67 (0.19), residues: 1950 helix: 0.56 (0.16), residues: 1085 sheet: 1.05 (0.31), residues: 270 loop : 0.23 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 21 TYR 0.017 0.001 TYR C 124 PHE 0.013 0.001 PHE F 307 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (16603) covalent geometry : angle 0.56161 / 0.29 (22607) hydrogen bonds : bond 0.05160 / 3.39 ( 807) hydrogen bonds : angle 4.99500 / 3.51 ( 2273) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 0.801 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 163 MET cc_start: 0.8943 (mmm) cc_final: 0.8738 (mmp) REVERT: A 291 ARG cc_start: 0.7996 (tpt-90) cc_final: 0.7697 (tpt-90) REVERT: A 296 ASP cc_start: 0.7994 (m-30) cc_final: 0.7779 (m-30) REVERT: C 90 LYS cc_start: 0.8124 (pttt) cc_final: 0.7823 (pttm) REVERT: C 105 ASP cc_start: 0.8469 (m-30) cc_final: 0.8250 (m-30) REVERT: C 325 MET cc_start: 0.9002 (mmp) cc_final: 0.8648 (mmp) REVERT: D 21 ARG cc_start: 0.7549 (tpp80) cc_final: 0.7109 (mmp-170) REVERT: D 171 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.8397 (mpt90) REVERT: D 309 MET cc_start: 0.9023 (mtp) cc_final: 0.8767 (mtp) REVERT: E 110 ASP cc_start: 0.9063 (t0) cc_final: 0.8852 (t0) REVERT: E 272 MET cc_start: 0.8331 (mtt) cc_final: 0.8019 (mtt) REVERT: F 213 SER cc_start: 0.9022 (t) cc_final: 0.8822 (p) REVERT: F 295 GLU cc_start: 0.8540 (tt0) cc_final: 0.8010 (tt0) REVERT: G 160 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7818 (tm-30) REVERT: G 161 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8022 (mm-40) REVERT: G 176 GLU cc_start: 0.8568 (tp30) cc_final: 0.7819 (tp30) REVERT: G 203 LEU cc_start: 0.6977 (tp) cc_final: 0.6742 (tp) outliers start: 21 outliers final: 16 residues processed: 265 average time/residue: 0.3222 time to fit residues: 120.9642 Evaluate side-chains 263 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 247 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain H residue 195 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 184 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN B 79 ASN D 166 ASN H 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.089040 restraints weight = 70604.544| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.25 r_work: 0.2799 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16603 Z= 0.186 Angle : 0.575 6.113 22607 Z= 0.299 Chirality : 0.041 0.144 2548 Planarity : 0.005 0.045 2808 Dihedral : 14.057 127.487 2626 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.52 % Allowed : 8.35 % Favored : 90.13 % 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: 0.62 (0.19), residues: 1950 helix: 0.55 (0.16), residues: 1090 sheet: 0.98 (0.31), residues: 270 loop : 0.17 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 179 TYR 0.019 0.001 TYR C 124 PHE 0.009 0.001 PHE B 58 HIS 0.004 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (16603) covalent geometry : angle 0.57543 / 0.30 (22607) hydrogen bonds : bond 0.05516 / 3.64 ( 807) hydrogen bonds : angle 4.96773 / 3.50 ( 2273) *********************** 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 276 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8351 (tpp) cc_final: 0.7944 (ttp) REVERT: C 90 LYS cc_start: 0.8002 (pttt) cc_final: 0.7704 (pttm) REVERT: C 325 MET cc_start: 0.9000 (mmp) cc_final: 0.8636 (mmp) REVERT: D 68 MET cc_start: 0.9379 (tpt) cc_final: 0.8614 (tpt) REVERT: D 143 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7421 (mtm-85) REVERT: D 171 ARG cc_start: 0.8711 (mmt-90) cc_final: 0.8355 (mpt90) REVERT: D 309 MET cc_start: 0.9055 (mtp) cc_final: 0.8803 (mtp) REVERT: E 110 ASP cc_start: 0.9051 (t0) cc_final: 0.8819 (t0) REVERT: E 254 ASP cc_start: 0.8860 (t0) cc_final: 0.8505 (t0) REVERT: E 272 MET cc_start: 0.8408 (mtt) cc_final: 0.7990 (mtt) REVERT: F 211 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8442 (ttp-110) REVERT: F 213 SER cc_start: 0.9039 (t) cc_final: 0.8804 (p) REVERT: F 295 GLU cc_start: 0.8510 (tt0) cc_final: 0.7925 (tt0) REVERT: G 203 LEU cc_start: 0.6920 (tp) cc_final: 0.6687 (tp) outliers start: 25 outliers final: 19 residues processed: 262 average time/residue: 0.3060 time to fit residues: 113.4795 Evaluate side-chains 261 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 241 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain H residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 286 ASN D 166 ASN D 286 ASN H 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.089837 restraints weight = 69996.108| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.27 r_work: 0.2884 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16603 Z= 0.132 Angle : 0.553 6.159 22607 Z= 0.285 Chirality : 0.040 0.163 2548 Planarity : 0.004 0.045 2808 Dihedral : 13.943 122.914 2626 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.98 % Allowed : 9.38 % Favored : 89.64 % 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: 0.78 (0.19), residues: 1950 helix: 0.74 (0.16), residues: 1083 sheet: 0.96 (0.32), residues: 265 loop : 0.14 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 267 TYR 0.017 0.001 TYR C 124 PHE 0.007 0.001 PHE B 58 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16603) covalent geometry : angle 0.55290 / 0.29 (22607) hydrogen bonds : bond 0.04848 / 3.20 ( 807) hydrogen bonds : angle 4.81060 / 3.40 ( 2273) *********************** 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 : 0.751 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 297 MET cc_start: 0.8344 (tpp) cc_final: 0.7985 (ttp) REVERT: C 90 LYS cc_start: 0.8117 (pttt) cc_final: 0.7818 (pttm) REVERT: D 21 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7151 (mmm160) REVERT: D 143 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7360 (mtm-85) REVERT: D 171 ARG cc_start: 0.8663 (mmt-90) cc_final: 0.8350 (mpt90) REVERT: D 309 MET cc_start: 0.9019 (mtp) cc_final: 0.8766 (mtp) REVERT: E 110 ASP cc_start: 0.9082 (t0) cc_final: 0.8872 (t0) REVERT: E 254 ASP cc_start: 0.8828 (t0) cc_final: 0.8584 (t0) REVERT: E 272 MET cc_start: 0.8412 (mtt) cc_final: 0.8040 (mtt) REVERT: F 105 ASP cc_start: 0.8554 (m-30) cc_final: 0.8306 (m-30) REVERT: F 213 SER cc_start: 0.9058 (t) cc_final: 0.8813 (p) REVERT: F 295 GLU cc_start: 0.8443 (tt0) cc_final: 0.7916 (tt0) REVERT: G 160 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7585 (tm-30) REVERT: G 161 GLN cc_start: 0.8583 (mm-40) cc_final: 0.7974 (mm-40) REVERT: G 203 LEU cc_start: 0.6976 (tp) cc_final: 0.6750 (tp) outliers start: 16 outliers final: 11 residues processed: 256 average time/residue: 0.3121 time to fit residues: 113.0368 Evaluate side-chains 254 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 243 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 129 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 286 ASN B 79 ASN D 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.089426 restraints weight = 70258.032| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.24 r_work: 0.2885 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16603 Z= 0.151 Angle : 0.556 8.109 22607 Z= 0.287 Chirality : 0.040 0.143 2548 Planarity : 0.004 0.045 2808 Dihedral : 13.899 122.329 2626 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.04 % Allowed : 9.38 % Favored : 89.58 % 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: 0.81 (0.19), residues: 1950 helix: 0.80 (0.16), residues: 1084 sheet: 0.91 (0.32), residues: 265 loop : 0.11 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 291 TYR 0.018 0.001 TYR C 124 PHE 0.008 0.001 PHE B 58 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (16603) covalent geometry : angle 0.55609 / 0.29 (22607) hydrogen bonds : bond 0.04861 / 3.21 ( 807) hydrogen bonds : angle 4.76797 / 3.37 ( 2273) *********************** 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 263 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 0.787 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 297 MET cc_start: 0.8404 (tpp) cc_final: 0.8110 (ttp) REVERT: C 90 LYS cc_start: 0.8116 (pttt) cc_final: 0.7811 (pttm) REVERT: D 143 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7303 (mtm-85) REVERT: D 171 ARG cc_start: 0.8633 (mmt-90) cc_final: 0.8321 (mpt90) REVERT: D 309 MET cc_start: 0.9012 (mtp) cc_final: 0.8787 (mtp) REVERT: E 110 ASP cc_start: 0.9081 (t0) cc_final: 0.8876 (t0) REVERT: E 254 ASP cc_start: 0.8844 (t0) cc_final: 0.8595 (t0) REVERT: E 272 MET cc_start: 0.8431 (mtt) cc_final: 0.8060 (mtt) REVERT: F 105 ASP cc_start: 0.8552 (m-30) cc_final: 0.8303 (m-30) REVERT: F 213 SER cc_start: 0.9114 (t) cc_final: 0.8844 (p) REVERT: F 267 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8199 (ttp-110) REVERT: F 295 GLU cc_start: 0.8448 (tt0) cc_final: 0.7918 (tt0) REVERT: G 160 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7768 (tm-30) REVERT: G 161 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8114 (mm-40) REVERT: G 203 LEU cc_start: 0.6986 (tp) cc_final: 0.6756 (tp) outliers start: 17 outliers final: 15 residues processed: 257 average time/residue: 0.3291 time to fit residues: 119.7905 Evaluate side-chains 261 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 246 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 129 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 57 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.089099 restraints weight = 70262.632| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.24 r_work: 0.2799 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16603 Z= 0.157 Angle : 0.558 7.196 22607 Z= 0.289 Chirality : 0.040 0.163 2548 Planarity : 0.005 0.045 2808 Dihedral : 13.876 126.296 2626 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.91 % Allowed : 9.69 % 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: 0.81 (0.19), residues: 1950 helix: 0.84 (0.16), residues: 1084 sheet: 0.92 (0.32), residues: 264 loop : 0.03 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.018 0.001 TYR C 124 PHE 0.008 0.001 PHE B 58 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (16603) covalent geometry : angle 0.55848 / 0.29 (22607) hydrogen bonds : bond 0.04849 / 3.21 ( 807) hydrogen bonds : angle 4.73112 / 3.34 ( 2273) *********************** 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 267 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 0.824 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 297 MET cc_start: 0.8424 (tpp) cc_final: 0.8091 (ttp) REVERT: C 90 LYS cc_start: 0.8007 (pttt) cc_final: 0.7680 (pttm) REVERT: C 133 ASP cc_start: 0.8248 (t0) cc_final: 0.7879 (p0) REVERT: D 143 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7290 (mtm-85) REVERT: D 171 ARG cc_start: 0.8629 (mmt-90) cc_final: 0.8305 (mpt90) REVERT: D 309 MET cc_start: 0.9001 (mtp) cc_final: 0.8781 (mtp) REVERT: E 110 ASP cc_start: 0.9043 (t0) cc_final: 0.8816 (t0) REVERT: E 254 ASP cc_start: 0.8887 (t0) cc_final: 0.8529 (t0) REVERT: E 272 MET cc_start: 0.8430 (mtt) cc_final: 0.8068 (mtt) REVERT: F 105 ASP cc_start: 0.8549 (m-30) cc_final: 0.8268 (m-30) REVERT: F 213 SER cc_start: 0.9112 (t) cc_final: 0.8791 (p) REVERT: F 267 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.8133 (ttp-110) REVERT: F 272 MET cc_start: 0.8400 (mmp) cc_final: 0.7944 (mmm) REVERT: F 295 GLU cc_start: 0.8457 (tt0) cc_final: 0.7923 (tt0) REVERT: G 160 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7752 (tm-30) REVERT: G 161 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8113 (mm-40) REVERT: G 203 LEU cc_start: 0.6990 (tp) cc_final: 0.6758 (tp) outliers start: 15 outliers final: 9 residues processed: 261 average time/residue: 0.3131 time to fit residues: 115.8538 Evaluate side-chains 253 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 244 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 169 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 154 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 286 ASN D 286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.089493 restraints weight = 69578.041| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.22 r_work: 0.2881 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16603 Z= 0.144 Angle : 0.561 9.164 22607 Z= 0.289 Chirality : 0.040 0.175 2548 Planarity : 0.005 0.044 2808 Dihedral : 13.844 128.754 2626 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.91 % Allowed : 9.93 % Favored : 89.15 % 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: 0.87 (0.19), residues: 1950 helix: 0.91 (0.16), residues: 1083 sheet: 0.94 (0.32), residues: 261 loop : 0.02 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 267 TYR 0.017 0.001 TYR C 124 PHE 0.008 0.001 PHE B 58 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (16603) covalent geometry : angle 0.56134 / 0.29 (22607) hydrogen bonds : bond 0.04683 / 3.10 ( 807) hydrogen bonds : angle 4.68341 / 3.31 ( 2273) *********************** 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 267 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 0.599 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 297 MET cc_start: 0.8342 (tpp) cc_final: 0.8103 (ttp) REVERT: C 90 LYS cc_start: 0.8186 (pttt) cc_final: 0.7869 (pttm) REVERT: C 133 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7874 (p0) REVERT: D 143 ARG cc_start: 0.7644 (mtm-85) cc_final: 0.7293 (mtm-85) REVERT: D 171 ARG cc_start: 0.8606 (mmt-90) cc_final: 0.8283 (mpt90) REVERT: D 309 MET cc_start: 0.8939 (mtp) cc_final: 0.8715 (mtp) REVERT: E 98 LEU cc_start: 0.9237 (mt) cc_final: 0.9001 (mm) REVERT: E 110 ASP cc_start: 0.9062 (t0) cc_final: 0.8854 (t0) REVERT: E 254 ASP cc_start: 0.8819 (t0) cc_final: 0.8568 (t0) REVERT: E 272 MET cc_start: 0.8379 (mtt) cc_final: 0.8007 (mtt) REVERT: F 105 ASP cc_start: 0.8538 (m-30) cc_final: 0.8291 (m-30) REVERT: F 213 SER cc_start: 0.9173 (t) cc_final: 0.8831 (p) REVERT: F 267 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8180 (ttp-110) REVERT: F 272 MET cc_start: 0.8318 (mmp) cc_final: 0.7887 (mmm) REVERT: F 295 GLU cc_start: 0.8438 (tt0) cc_final: 0.7923 (tt0) REVERT: G 160 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7788 (tm-30) REVERT: G 161 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8107 (mm-40) REVERT: G 203 LEU cc_start: 0.7079 (tp) cc_final: 0.6850 (tp) outliers start: 15 outliers final: 14 residues processed: 260 average time/residue: 0.3009 time to fit residues: 111.0869 Evaluate side-chains 263 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 248 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 129 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 102 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 128 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.090699 restraints weight = 69773.036| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.23 r_work: 0.2906 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16603 Z= 0.109 Angle : 0.556 10.757 22607 Z= 0.284 Chirality : 0.039 0.131 2548 Planarity : 0.005 0.075 2808 Dihedral : 13.762 126.976 2626 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.85 % Allowed : 10.18 % Favored : 88.97 % 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: 1.07 (0.19), residues: 1950 helix: 1.07 (0.17), residues: 1083 sheet: 0.99 (0.32), residues: 261 loop : 0.14 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 179 TYR 0.014 0.001 TYR C 124 PHE 0.006 0.001 PHE B 58 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (16603) covalent geometry : angle 0.55552 / 0.28 (22607) hydrogen bonds : bond 0.04145 / 2.73 ( 807) hydrogen bonds : angle 4.58717 / 3.24 ( 2273) ********************** 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 268 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 254 time to evaluate : 0.757 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 158 THR cc_start: 0.9369 (t) cc_final: 0.9004 (m) REVERT: A 297 MET cc_start: 0.8288 (tpp) cc_final: 0.8051 (ttp) REVERT: C 90 LYS cc_start: 0.8177 (pttt) cc_final: 0.7867 (pttm) REVERT: C 133 ASP cc_start: 0.8053 (t0) cc_final: 0.7775 (p0) REVERT: D 143 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7286 (mtm-85) REVERT: D 171 ARG cc_start: 0.8568 (mmt-90) cc_final: 0.8170 (mpt90) REVERT: D 309 MET cc_start: 0.8870 (mtp) cc_final: 0.8643 (mtp) REVERT: E 81 LYS cc_start: 0.8331 (mttt) cc_final: 0.7870 (tptt) REVERT: E 110 ASP cc_start: 0.9065 (t0) cc_final: 0.8854 (t0) REVERT: E 254 ASP cc_start: 0.8769 (t0) cc_final: 0.8550 (t0) REVERT: E 272 MET cc_start: 0.8349 (mtt) cc_final: 0.7984 (mtt) REVERT: F 105 ASP cc_start: 0.8556 (m-30) cc_final: 0.8314 (m-30) REVERT: F 213 SER cc_start: 0.9138 (t) cc_final: 0.8770 (p) REVERT: F 267 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8162 (ttp-110) REVERT: F 272 MET cc_start: 0.8285 (mmp) cc_final: 0.7851 (mmm) REVERT: F 295 GLU cc_start: 0.8412 (tt0) cc_final: 0.7908 (tt0) REVERT: G 160 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7777 (tm-30) REVERT: G 161 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8111 (mm-40) REVERT: G 203 LEU cc_start: 0.7110 (tp) cc_final: 0.6876 (tp) outliers start: 14 outliers final: 13 residues processed: 263 average time/residue: 0.2986 time to fit residues: 112.7567 Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 247 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.089969 restraints weight = 69713.649| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.21 r_work: 0.2838 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16603 Z= 0.126 Angle : 0.550 10.013 22607 Z= 0.280 Chirality : 0.039 0.134 2548 Planarity : 0.004 0.048 2808 Dihedral : 13.739 128.683 2626 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.85 % Allowed : 10.42 % Favored : 88.73 % 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: 1.10 (0.19), residues: 1950 helix: 1.13 (0.17), residues: 1083 sheet: 0.93 (0.32), residues: 261 loop : 0.12 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 179 TYR 0.016 0.001 TYR C 124 PHE 0.007 0.001 PHE B 58 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16603) covalent geometry : angle 0.54985 / 0.28 (22607) hydrogen bonds : bond 0.04242 / 2.81 ( 807) hydrogen bonds : angle 4.57181 / 3.23 ( 2273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6993.80 seconds wall clock time: 118 minutes 55.47 seconds (7135.47 seconds total)