Starting phenix.real_space_refine on Fri Mar 6 15:34:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbn_13296/03_2026/7pbn_13296_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbn_13296/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pbn_13296/03_2026/7pbn_13296_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbn_13296/03_2026/7pbn_13296_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbn_13296/03_2026/7pbn_13296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbn_13296/03_2026/7pbn_13296.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 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-5986/lib/python3.9/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: 5.51, per 1000 atoms: 0.17 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: 2.69 Conformation dependent library (CDL) restraints added in 958.4 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: 5.46 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: 7.59 Time building geometry restraints manager: 3.46 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 - 1.96: 57954 1.96 - 3.93: 653 3.93 - 5.89: 57 5.89 - 7.85: 13 7.85 - 9.82: 7 Bond angle restraints: 58684 Sorted by residual: angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 110.18 9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA TYR C 124 " pdb=" CB TYR C 124 " pdb=" CG TYR C 124 " ideal model delta sigma weight residual 113.90 119.70 -5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" C4' DC V 8 " pdb=" O4' DC V 8 " pdb=" C1' DC V 8 " ideal model delta sigma weight residual 109.70 105.14 4.56 1.50e+00 4.44e-01 9.24e+00 angle pdb=" C1' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C3' ADP D 600 " ideal model delta sigma weight residual 111.00 102.43 8.57 3.00e+00 1.11e-01 8.15e+00 angle pdb=" C1' ADP E 600 " pdb=" C2' ADP E 600 " pdb=" C3' ADP E 600 " ideal model delta sigma weight residual 111.00 102.44 8.56 3.00e+00 1.11e-01 8.15e+00 ... (remaining 58679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.28: 14411 31.28 - 62.57: 581 62.57 - 93.85: 31 93.85 - 125.14: 2 125.14 - 156.42: 5 Dihedral angle restraints: 15030 sinusoidal: 8597 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 15027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2280 0.070 - 0.139: 266 0.139 - 0.209: 5 0.209 - 0.278: 0 0.278 - 0.348: 1 Chirality restraints: 2552 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.69 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA TYR C 124 " pdb=" N TYR C 124 " pdb=" C TYR C 124 " pdb=" CB TYR C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA ARG E 214 " pdb=" N ARG E 214 " pdb=" C ARG E 214 " pdb=" CB ARG E 214 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 2549 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: 3.600 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: 0.170 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.200 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 0.039 16603 Z= 0.167 Angle : 0.727 9.817 22607 Z= 0.410 Chirality : 0.044 0.348 2552 Planarity : 0.010 0.153 2808 Dihedral : 14.915 156.423 6403 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 covalent geometry : bond 0.00382 (16603) covalent geometry : angle 0.72656 (22607) hydrogen bonds : bond 0.25940 ( 807) hydrogen bonds : angle 8.43706 ( 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 : 0.794 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: 0.3851 time to fit residues: 213.5485 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 : 0.677 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN C 99 ASN D 166 ASN D 246 GLN D 286 ASN F 255 HIS H 161 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090762 restraints weight = 70846.592| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.28 r_work: 0.2880 rms_B_bonded: 2.53 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: 0.8544 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16603 Z= 0.168 Angle : 0.635 6.753 22607 Z= 0.340 Chirality : 0.041 0.152 2552 Planarity : 0.005 0.049 2808 Dihedral : 14.692 143.792 2590 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.91 % Allowed : 6.52 % Favored : 92.57 % 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: 0.16 (0.18), residues: 1950 helix: -0.03 (0.15), residues: 1079 sheet: 1.07 (0.31), residues: 271 loop : 0.25 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 143 TYR 0.019 0.001 TYR C 124 PHE 0.009 0.001 PHE C 25 HIS 0.008 0.001 HIS F 255 Details of bonding type rmsd covalent geometry : bond 0.00361 (16603) covalent geometry : angle 0.63522 (22607) hydrogen bonds : bond 0.07273 ( 807) hydrogen bonds : angle 5.80409 ( 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 286 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 271 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.9314 (mmm) cc_final: 0.9104 (mmt) REVERT: A 163 MET cc_start: 0.8958 (mmm) cc_final: 0.8743 (mmp) REVERT: A 291 ARG cc_start: 0.8035 (tpt-90) cc_final: 0.7804 (tpt-90) REVERT: A 296 ASP cc_start: 0.8095 (m-30) cc_final: 0.7859 (m-30) REVERT: B 105 ASP cc_start: 0.8462 (m-30) cc_final: 0.8213 (m-30) REVERT: C 90 LYS cc_start: 0.8144 (pttt) cc_final: 0.7877 (pttm) REVERT: C 105 ASP cc_start: 0.8441 (m-30) cc_final: 0.8238 (m-30) REVERT: C 178 MET cc_start: 0.9267 (mmt) cc_final: 0.8112 (mmt) REVERT: C 325 MET cc_start: 0.9039 (mmp) cc_final: 0.8770 (mmp) REVERT: D 171 ARG cc_start: 0.8689 (mmt-90) cc_final: 0.8394 (mpt90) REVERT: D 309 MET cc_start: 0.9009 (mtp) cc_final: 0.8735 (mtp) REVERT: E 241 ASP cc_start: 0.7240 (p0) cc_final: 0.7027 (t0) REVERT: E 256 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7974 (mm-30) REVERT: E 272 MET cc_start: 0.8355 (mtt) cc_final: 0.8028 (mtt) REVERT: F 211 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8462 (ttp-110) REVERT: F 295 GLU cc_start: 0.8458 (tt0) cc_final: 0.7901 (tt0) REVERT: G 203 LEU cc_start: 0.6934 (tp) cc_final: 0.6726 (tp) outliers start: 15 outliers final: 13 residues processed: 278 average time/residue: 0.3307 time to fit residues: 128.0882 Evaluate side-chains 269 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 255 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 284 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 0.0970 chunk 160 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 181 optimal weight: 0.3980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 HIS D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.091549 restraints weight = 70226.607| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.23 r_work: 0.2862 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2900 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= 0.131 Angle : 0.562 5.954 22607 Z= 0.293 Chirality : 0.040 0.155 2552 Planarity : 0.004 0.047 2808 Dihedral : 14.521 136.083 2590 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.34 % Allowed : 7.25 % Favored : 91.41 % 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: 0.53 (0.19), residues: 1950 helix: 0.41 (0.16), residues: 1084 sheet: 1.06 (0.30), residues: 270 loop : 0.20 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 291 TYR 0.017 0.001 TYR C 124 PHE 0.006 0.001 PHE C 108 HIS 0.003 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00287 (16603) covalent geometry : angle 0.56197 (22607) hydrogen bonds : bond 0.05720 ( 807) hydrogen bonds : angle 5.17961 ( 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 282 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.9283 (mmm) cc_final: 0.9055 (mmt) REVERT: A 291 ARG cc_start: 0.7991 (tpt-90) cc_final: 0.7740 (tpt-90) REVERT: C 90 LYS cc_start: 0.8154 (pttt) cc_final: 0.7891 (pttm) REVERT: C 135 MET cc_start: 0.4567 (mmm) cc_final: 0.4120 (mmm) REVERT: C 178 MET cc_start: 0.9255 (mmt) cc_final: 0.8137 (mmt) REVERT: C 325 MET cc_start: 0.9034 (mmp) cc_final: 0.8698 (mmp) REVERT: D 171 ARG cc_start: 0.8708 (mmt-90) cc_final: 0.8395 (mpt90) REVERT: D 309 MET cc_start: 0.8993 (mtp) cc_final: 0.8718 (mtp) REVERT: E 241 ASP cc_start: 0.7210 (p0) cc_final: 0.7003 (t0) REVERT: E 256 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8266 (mm-30) REVERT: E 272 MET cc_start: 0.8329 (mtt) cc_final: 0.8028 (mtt) REVERT: F 105 ASP cc_start: 0.8168 (m-30) cc_final: 0.7873 (m-30) REVERT: F 295 GLU cc_start: 0.8542 (tt0) cc_final: 0.7934 (tt0) REVERT: F 329 TYR cc_start: 0.8094 (t80) cc_final: 0.7528 (t80) REVERT: G 203 LEU cc_start: 0.6953 (tp) cc_final: 0.6734 (tp) outliers start: 22 outliers final: 15 residues processed: 272 average time/residue: 0.3231 time to fit residues: 123.0822 Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 245 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 105 ASP 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 E residue 284 SER Chi-restraints excluded: chain F residue 129 ASP 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: 0.5980 chunk 185 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 110 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.091541 restraints weight = 70352.945| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.22 r_work: 0.2878 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3223 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= 0.128 Angle : 0.545 6.593 22607 Z= 0.282 Chirality : 0.040 0.156 2552 Planarity : 0.004 0.039 2808 Dihedral : 14.341 139.169 2590 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.34 % Allowed : 8.23 % Favored : 90.43 % 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: 0.93 (0.19), residues: 1950 helix: 0.75 (0.16), residues: 1084 sheet: 1.10 (0.31), residues: 270 loop : 0.42 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 21 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 covalent geometry : bond 0.00288 (16603) covalent geometry : angle 0.54535 (22607) hydrogen bonds : bond 0.04677 ( 807) hydrogen bonds : angle 4.84990 ( 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 281 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 259 time to evaluate : 0.800 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 291 ARG cc_start: 0.8003 (tpt-90) cc_final: 0.7718 (tpt-90) REVERT: B 242 LYS cc_start: 0.8776 (tppp) cc_final: 0.8542 (mmtt) REVERT: C 90 LYS cc_start: 0.8098 (pttt) cc_final: 0.7836 (pttm) REVERT: C 325 MET cc_start: 0.9007 (mmp) cc_final: 0.8632 (mmp) REVERT: D 21 ARG cc_start: 0.7518 (tpp80) cc_final: 0.7163 (mmm160) REVERT: D 76 MET cc_start: 0.8802 (mmm) cc_final: 0.8476 (tpt) REVERT: D 117 MET cc_start: 0.6920 (tmm) cc_final: 0.4781 (tmm) REVERT: D 171 ARG cc_start: 0.8668 (mmt-90) cc_final: 0.8345 (mpt90) REVERT: D 309 MET cc_start: 0.8962 (mtp) cc_final: 0.8688 (mtp) REVERT: E 110 ASP cc_start: 0.9024 (t0) cc_final: 0.8806 (t0) REVERT: E 256 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8297 (mm-30) REVERT: E 272 MET cc_start: 0.8303 (mtt) cc_final: 0.8009 (mtt) REVERT: F 105 ASP cc_start: 0.8215 (m-30) cc_final: 0.7907 (m-30) REVERT: F 211 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8421 (ttp-110) REVERT: F 295 GLU cc_start: 0.8547 (tt0) cc_final: 0.7976 (tt0) REVERT: G 203 LEU cc_start: 0.6939 (tp) cc_final: 0.6703 (tp) outliers start: 22 outliers final: 16 residues processed: 272 average time/residue: 0.3347 time to fit residues: 127.3324 Evaluate side-chains 261 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE 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 211 ARG Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 184 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN H 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.089591 restraints weight = 70558.879| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.25 r_work: 0.2859 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16603 Z= 0.164 Angle : 0.556 6.008 22607 Z= 0.288 Chirality : 0.040 0.140 2552 Planarity : 0.005 0.043 2808 Dihedral : 14.298 140.610 2590 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.46 % Allowed : 8.84 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1950 helix: 0.77 (0.16), residues: 1084 sheet: 0.98 (0.32), residues: 265 loop : 0.27 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.018 0.001 TYR C 124 PHE 0.009 0.001 PHE F 307 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00383 (16603) covalent geometry : angle 0.55572 (22607) hydrogen bonds : bond 0.05004 ( 807) hydrogen bonds : angle 4.80702 ( 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 273 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 249 time to evaluate : 0.781 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: A 297 MET cc_start: 0.8387 (tpp) cc_final: 0.8001 (ttp) REVERT: C 90 LYS cc_start: 0.8116 (pttt) cc_final: 0.7805 (pttm) REVERT: D 76 MET cc_start: 0.8823 (mmm) cc_final: 0.8582 (tpt) REVERT: D 143 ARG cc_start: 0.7626 (mtm-85) cc_final: 0.7319 (mtm-85) REVERT: D 171 ARG cc_start: 0.8644 (mmt-90) cc_final: 0.8344 (mpt90) REVERT: D 309 MET cc_start: 0.9035 (mtp) cc_final: 0.8770 (mtp) REVERT: E 110 ASP cc_start: 0.9076 (t0) cc_final: 0.8872 (t0) REVERT: E 272 MET cc_start: 0.8371 (mtt) cc_final: 0.7946 (mtt) REVERT: F 295 GLU cc_start: 0.8457 (tt0) cc_final: 0.7935 (tt0) REVERT: G 203 LEU cc_start: 0.6962 (tp) cc_final: 0.6720 (tp) outliers start: 24 outliers final: 20 residues processed: 260 average time/residue: 0.3347 time to fit residues: 121.2669 Evaluate side-chains 263 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 233 ILE 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 163 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 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 83 THR 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 199 MET Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 287 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: 3.9990 chunk 3 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 286 ASN H 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.089802 restraints weight = 69812.765| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.24 r_work: 0.2871 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3442 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= 0.146 Angle : 0.542 6.191 22607 Z= 0.279 Chirality : 0.040 0.161 2552 Planarity : 0.004 0.042 2808 Dihedral : 14.214 143.445 2590 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.16 % Allowed : 9.14 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1950 helix: 0.88 (0.16), residues: 1085 sheet: 0.98 (0.32), residues: 265 loop : 0.21 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.017 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 covalent geometry : bond 0.00338 (16603) covalent geometry : angle 0.54207 (22607) hydrogen bonds : bond 0.04648 ( 807) hydrogen bonds : angle 4.69619 ( 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 269 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 250 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8424 (tpp) cc_final: 0.8052 (ttp) REVERT: C 90 LYS cc_start: 0.8106 (pttt) cc_final: 0.7802 (pttm) REVERT: C 135 MET cc_start: 0.4535 (mmm) cc_final: 0.4135 (mmm) REVERT: D 76 MET cc_start: 0.8818 (mmm) cc_final: 0.8555 (tpt) REVERT: D 143 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7277 (mtm-85) REVERT: D 171 ARG cc_start: 0.8641 (mmt-90) cc_final: 0.8319 (mpt90) REVERT: D 286 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8485 (m110) REVERT: D 309 MET cc_start: 0.8988 (mtp) cc_final: 0.8721 (mtp) REVERT: E 272 MET cc_start: 0.8392 (mtt) cc_final: 0.8013 (mtt) REVERT: F 211 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8492 (ttp-110) REVERT: F 295 GLU cc_start: 0.8449 (tt0) cc_final: 0.7940 (tt0) REVERT: G 203 LEU cc_start: 0.7008 (tp) cc_final: 0.6772 (tp) outliers start: 19 outliers final: 12 residues processed: 263 average time/residue: 0.3401 time to fit residues: 124.3390 Evaluate side-chains 259 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 245 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 233 ILE 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 D residue 286 ASN 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 Chi-restraints excluded: chain F residue 211 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.090035 restraints weight = 70177.066| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.24 r_work: 0.2876 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16603 Z= 0.130 Angle : 0.535 6.172 22607 Z= 0.276 Chirality : 0.039 0.152 2552 Planarity : 0.004 0.041 2808 Dihedral : 14.139 144.497 2590 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.28 % Allowed : 9.02 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 1950 helix: 0.98 (0.16), residues: 1085 sheet: 0.99 (0.32), residues: 265 loop : 0.23 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 291 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 covalent geometry : bond 0.00297 (16603) covalent geometry : angle 0.53477 (22607) hydrogen bonds : bond 0.04388 ( 807) hydrogen bonds : angle 4.62385 ( 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 271 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8415 (tpp) cc_final: 0.8057 (ttp) REVERT: C 90 LYS cc_start: 0.8166 (pttt) cc_final: 0.7847 (pttm) REVERT: C 105 ASP cc_start: 0.8074 (m-30) cc_final: 0.7742 (m-30) REVERT: D 76 MET cc_start: 0.8790 (mmm) cc_final: 0.8518 (tpt) REVERT: D 143 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7305 (mtm-85) REVERT: D 171 ARG cc_start: 0.8586 (mmt-90) cc_final: 0.8242 (mpt90) REVERT: D 309 MET cc_start: 0.8942 (mtp) cc_final: 0.8738 (mtp) REVERT: E 272 MET cc_start: 0.8380 (mtt) cc_final: 0.8003 (mtt) REVERT: F 295 GLU cc_start: 0.8454 (tt0) cc_final: 0.7944 (tt0) REVERT: G 176 GLU cc_start: 0.8651 (tp30) cc_final: 0.7683 (tp30) REVERT: G 203 LEU cc_start: 0.7050 (tp) cc_final: 0.6818 (tp) outliers start: 21 outliers final: 18 residues processed: 266 average time/residue: 0.3193 time to fit residues: 119.9700 Evaluate side-chains 265 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 233 ILE 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 83 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 84 SER 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 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: 0.9990 chunk 165 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 67 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 185 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.090705 restraints weight = 69844.986| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.21 r_work: 0.2865 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16603 Z= 0.110 Angle : 0.534 8.404 22607 Z= 0.273 Chirality : 0.039 0.154 2552 Planarity : 0.004 0.039 2808 Dihedral : 14.034 145.748 2590 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.16 % Allowed : 9.38 % Favored : 89.46 % 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: 1.21 (0.19), residues: 1950 helix: 1.15 (0.16), residues: 1084 sheet: 1.07 (0.32), residues: 261 loop : 0.26 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.015 0.001 TYR C 124 PHE 0.007 0.001 PHE E 25 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00247 (16603) covalent geometry : angle 0.53375 (22607) hydrogen bonds : bond 0.03984 ( 807) hydrogen bonds : angle 4.52704 ( 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 274 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 255 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 THR cc_start: 0.9380 (t) cc_final: 0.9038 (m) REVERT: A 297 MET cc_start: 0.8370 (tpp) cc_final: 0.8065 (ttp) REVERT: C 90 LYS cc_start: 0.8196 (pttt) cc_final: 0.7871 (pttm) REVERT: C 105 ASP cc_start: 0.8094 (m-30) cc_final: 0.7776 (m-30) REVERT: C 133 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7829 (p0) REVERT: C 135 MET cc_start: 0.4612 (mmm) cc_final: 0.4263 (mmm) REVERT: D 76 MET cc_start: 0.8748 (mmm) cc_final: 0.8462 (tpt) REVERT: D 143 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.7275 (mtm-85) REVERT: D 171 ARG cc_start: 0.8546 (mmt-90) cc_final: 0.8137 (mpt90) REVERT: D 309 MET cc_start: 0.8913 (mtp) cc_final: 0.8684 (mtp) REVERT: E 81 LYS cc_start: 0.8330 (mttt) cc_final: 0.7879 (tptt) REVERT: E 272 MET cc_start: 0.8374 (mtt) cc_final: 0.8003 (mtt) REVERT: F 291 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.7981 (ttm-80) REVERT: F 295 GLU cc_start: 0.8425 (tt0) cc_final: 0.7914 (tt0) REVERT: G 203 LEU cc_start: 0.6974 (tp) cc_final: 0.6747 (tp) outliers start: 19 outliers final: 18 residues processed: 267 average time/residue: 0.3379 time to fit residues: 126.1335 Evaluate side-chains 265 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 233 ILE 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 83 THR 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 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 E residue 199 MET 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: 2.9990 chunk 30 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3386 r_free = 0.3386 target = 0.115890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.089179 restraints weight = 69796.188| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.19 r_work: 0.2873 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3662 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 : 0.559 6.134 22607 Z= 0.288 Chirality : 0.040 0.153 2552 Planarity : 0.005 0.044 2808 Dihedral : 14.104 142.819 2590 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.16 % Allowed : 9.75 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.19), residues: 1950 helix: 1.07 (0.16), residues: 1081 sheet: 0.91 (0.32), residues: 260 loop : 0.16 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 291 TYR 0.020 0.001 TYR C 124 PHE 0.009 0.001 PHE B 58 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00419 (16603) covalent geometry : angle 0.55896 (22607) hydrogen bonds : bond 0.04791 ( 807) hydrogen bonds : angle 4.61621 ( 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 266 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8364 (tpp) cc_final: 0.8071 (ttp) REVERT: C 90 LYS cc_start: 0.8185 (pttt) cc_final: 0.7861 (pttm) REVERT: C 133 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7850 (p0) REVERT: C 135 MET cc_start: 0.4572 (mmm) cc_final: 0.4319 (mmm) REVERT: D 76 MET cc_start: 0.8798 (mmm) cc_final: 0.8525 (tpt) REVERT: D 117 MET cc_start: 0.6997 (tmm) cc_final: 0.6790 (tpt) REVERT: D 128 GLU cc_start: 0.8040 (tt0) cc_final: 0.7642 (tt0) REVERT: D 171 ARG cc_start: 0.8591 (mmt-90) cc_final: 0.8178 (mpt90) REVERT: D 309 MET cc_start: 0.8940 (mtp) cc_final: 0.8729 (mtp) REVERT: E 272 MET cc_start: 0.8392 (mtt) cc_final: 0.8010 (mtt) REVERT: F 295 GLU cc_start: 0.8414 (tt0) cc_final: 0.7914 (tt0) REVERT: G 203 LEU cc_start: 0.7035 (tp) cc_final: 0.6808 (tp) outliers start: 19 outliers final: 18 residues processed: 258 average time/residue: 0.3164 time to fit residues: 116.0570 Evaluate side-chains 262 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 233 ILE 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 83 THR 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 23 GLN Chi-restraints excluded: chain E residue 83 THR 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 E residue 199 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 102 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 128 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3401 r_free = 0.3401 target = 0.117065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.090153 restraints weight = 69994.241| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.22 r_work: 0.2850 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3755 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= 0.112 Angle : 0.534 6.283 22607 Z= 0.271 Chirality : 0.039 0.153 2552 Planarity : 0.004 0.046 2808 Dihedral : 13.995 145.991 2590 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.10 % Allowed : 10.12 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 1950 helix: 1.23 (0.17), residues: 1084 sheet: 0.99 (0.32), residues: 258 loop : 0.22 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 291 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 covalent geometry : bond 0.00253 (16603) covalent geometry : angle 0.53419 (22607) hydrogen bonds : bond 0.03974 ( 807) hydrogen bonds : angle 4.47649 ( 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 262 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 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 158 THR cc_start: 0.9359 (t) cc_final: 0.9004 (m) REVERT: A 297 MET cc_start: 0.8356 (tpp) cc_final: 0.8041 (ttp) REVERT: C 90 LYS cc_start: 0.8190 (pttt) cc_final: 0.7876 (pttm) REVERT: C 133 ASP cc_start: 0.8101 (t70) cc_final: 0.7787 (p0) REVERT: C 135 MET cc_start: 0.4659 (mmm) cc_final: 0.4325 (mmm) REVERT: D 76 MET cc_start: 0.8754 (mmm) cc_final: 0.8468 (tpt) REVERT: D 143 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7334 (mtm-85) REVERT: D 309 MET cc_start: 0.8874 (mtp) cc_final: 0.8660 (mtp) REVERT: E 81 LYS cc_start: 0.8361 (mttt) cc_final: 0.7881 (tptt) REVERT: E 272 MET cc_start: 0.8387 (mtt) cc_final: 0.8024 (mtt) REVERT: F 267 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8121 (ttp-110) REVERT: F 295 GLU cc_start: 0.8370 (tt0) cc_final: 0.7861 (tt0) REVERT: G 160 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7528 (tm-30) REVERT: G 203 LEU cc_start: 0.7000 (tp) cc_final: 0.6769 (tp) outliers start: 18 outliers final: 17 residues processed: 256 average time/residue: 0.3077 time to fit residues: 113.0184 Evaluate side-chains 259 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 233 ILE 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 83 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 84 SER 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 E residue 199 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 0.0030 chunk 14 optimal weight: 0.0670 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 overall best weight: 0.2846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091903 restraints weight = 69548.125| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.20 r_work: 0.2871 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16603 Z= 0.099 Angle : 0.519 6.365 22607 Z= 0.263 Chirality : 0.038 0.151 2552 Planarity : 0.004 0.045 2808 Dihedral : 13.895 146.437 2590 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.98 % Allowed : 10.66 % Favored : 88.36 % 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: 1.46 (0.20), residues: 1950 helix: 1.38 (0.17), residues: 1085 sheet: 1.06 (0.32), residues: 258 loop : 0.36 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.013 0.001 TYR C 124 PHE 0.006 0.001 PHE E 25 HIS 0.016 0.001 HIS H 206 Details of bonding type rmsd covalent geometry : bond 0.00221 (16603) covalent geometry : angle 0.51892 (22607) hydrogen bonds : bond 0.03547 ( 807) hydrogen bonds : angle 4.37182 ( 2273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7321.70 seconds wall clock time: 124 minutes 31.18 seconds (7471.18 seconds total)