Starting phenix.real_space_refine on Mon Sep 14 17:35:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbn_13296/09_2026/7pbn_13296_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbn_13296/09_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_13296/09_2026/7pbn_13296_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbn_13296/09_2026/7pbn_13296_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbn_13296/09_2026/7pbn_13296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbn_13296/09_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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32074 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 760 Classifications: {'peptide': 50} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.10, per 1000 atoms: 0.16 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: 2.97 Conformation dependent library (CDL) restraints added in 797.9 milliseconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 20 sheets defined 60.3% alpha, 10.9% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.517A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.760A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.541A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 removed outlier: 3.635A pdb=" N MET A 115 " --> pdb=" O ILE A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.886A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.676A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.661A pdb=" N GLU A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.874A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 removed outlier: 3.610A pdb=" N ILE A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 removed outlier: 3.540A pdb=" N VAL A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.659A pdb=" N GLU A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.746A pdb=" N LEU A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.603A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.523A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.611A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.600A pdb=" N GLU B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 removed outlier: 3.615A pdb=" N GLU B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 removed outlier: 3.508A pdb=" N TYR B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.652A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'C' and resid 31 through 48 Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.770A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.723A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.984A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 165 through 172 removed outlier: 3.535A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.570A pdb=" N ILE C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.558A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 235 removed outlier: 3.663A pdb=" N ILE C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.749A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 273 removed outlier: 3.521A pdb=" N LEU C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.843A pdb=" N LEU C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.611A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 77 Processing helix chain 'D' and resid 90 through 100 removed outlier: 3.736A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 130 removed outlier: 4.438A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.586A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.180A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.631A pdb=" N GLU D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 232 Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.556A pdb=" N GLY D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 removed outlier: 3.589A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.638A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'E' and resid 31 through 48 removed outlier: 3.621A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.748A pdb=" N PHE E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.543A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.769A pdb=" N MET E 115 " --> pdb=" O ILE E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 115' Processing helix chain 'E' and resid 116 through 130 removed outlier: 4.489A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.710A pdb=" N GLU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 213 Processing helix chain 'E' and resid 216 through 235 removed outlier: 3.634A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 removed outlier: 3.551A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 279 through 287 Processing helix chain 'E' and resid 290 through 298 removed outlier: 3.591A pdb=" N ASP E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.902A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.520A pdb=" N PHE F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 90 through 99 removed outlier: 3.649A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.731A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU F 128 " --> pdb=" O TYR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 removed outlier: 3.671A pdb=" N GLU F 188 " --> pdb=" O PRO F 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.874A pdb=" N GLU F 271 " --> pdb=" O ARG F 267 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.596A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 190 through 202 Processing helix chain 'H' and resid 159 through 170 Processing helix chain 'H' and resid 173 through 184 removed outlier: 3.744A pdb=" N ILE H 184 " --> pdb=" O MET H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 199 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.686A pdb=" N ASP A 110 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 removed outlier: 7.029A pdb=" N THR A 200 " --> pdb=" O ILE A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 84 removed outlier: 6.552A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 84 removed outlier: 6.258A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 56 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 84 removed outlier: 3.580A pdb=" N ASP D 110 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AB5, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.608A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU E 56 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 131 through 136 Processing sheet with id=AB7, first strand: chain 'E' and resid 200 through 201 removed outlier: 7.027A pdb=" N THR E 200 " --> pdb=" O ILE E 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 308 through 311 Processing sheet with id=AB9, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.245A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AC2, first strand: chain 'F' and resid 308 through 311 779 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 6.37 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 15818 1.06 - 1.28: 2721 1.28 - 1.50: 6867 1.50 - 1.72: 6817 1.72 - 1.94: 198 Bond restraints: 32421 Sorted by residual: bond pdb=" N THR F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASP H 158 " pdb=" H1 ASP H 158 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N SER G 156 " pdb=" H1 SER G 156 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 ... (remaining 32416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 57938 2.01 - 4.02: 654 4.02 - 6.03: 68 6.03 - 8.04: 9 8.04 - 10.06: 15 Bond angle restraints: 58684 Sorted by residual: angle pdb=" C4' DC V 8 " pdb=" O4' DC V 8 " pdb=" C1' DC V 8 " ideal model delta sigma weight residual 110.10 105.14 4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.24e+01 angle pdb=" C4' DT V 15 " pdb=" O4' DT V 15 " pdb=" C1' DT V 15 " ideal model delta sigma weight residual 110.10 105.93 4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" O4' DA U 13 " pdb=" C1' DA U 13 " pdb=" N9 DA U 13 " ideal model delta sigma weight residual 108.00 110.88 -2.88 7.00e-01 2.04e+00 1.70e+01 angle pdb=" N3 DT V 3 " pdb=" C4 DT V 3 " pdb=" O4 DT V 3 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 58679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.28: 14431 31.28 - 62.57: 590 62.57 - 93.85: 40 93.85 - 125.14: 1 125.14 - 156.42: 4 Dihedral angle restraints: 15066 sinusoidal: 8633 harmonic: 6433 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 96.42 -156.42 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 91.76 -151.76 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 79.17 -139.17 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 15063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2264 0.072 - 0.143: 266 0.143 - 0.215: 15 0.215 - 0.287: 2 0.287 - 0.358: 1 Chirality restraints: 2548 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.69 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C3' AGS B 401 " pdb=" C2' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" O3' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2545 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 218 " 0.037 9.50e-02 1.11e+02 5.02e-02 5.34e+01 pdb=" NE ARG F 218 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG F 218 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG F 218 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 218 " -0.093 2.00e-02 2.50e+03 pdb="HH11 ARG F 218 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 218 " -0.007 2.00e-02 2.50e+03 pdb="HH21 ARG F 218 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARG F 218 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 192 " 0.100 9.50e-02 1.11e+02 5.50e-02 4.40e+01 pdb=" NE ARG A 192 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG A 192 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 192 " 0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG A 192 " -0.074 2.00e-02 2.50e+03 pdb="HH11 ARG A 192 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 192 " -0.058 2.00e-02 2.50e+03 pdb="HH21 ARG A 192 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 192 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.039 2.00e-02 2.50e+03 4.82e-02 3.49e+01 pdb=" CD GLN C 31 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.077 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.002 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.074 2.00e-02 2.50e+03 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 693 2.13 - 2.75: 56276 2.75 - 3.36: 84673 3.36 - 3.98: 107981 3.98 - 4.60: 175389 Nonbonded interactions: 425012 Sorted by model distance: nonbonded pdb=" HG1 THR F 311 " pdb=" O GLY F 314 " model vdw 1.509 2.450 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.558 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.580 2.450 nonbonded pdb=" HZ3 LYS E 81 " pdb=" O ASP E 100 " model vdw 1.582 2.450 nonbonded pdb=" HG1 THR F 66 " pdb=" O1B ADP F 600 " model vdw 1.590 2.450 ... (remaining 425007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } ncs_group { reference = (chain 'G' and (resid 158 through 202 or (resid 203 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name H or name H \ A or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or n \ ame HD21 or name HD22 or name HD23)))) selection = (chain 'H' and resid 158 through 203) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 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: 0.200 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.320 Find NCS groups from input model: 0.670 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 16603 Z= 0.246 Angle : 0.777 10.056 22607 Z= 0.454 Chirality : 0.046 0.358 2548 Planarity : 0.010 0.153 2808 Dihedral : 15.085 156.423 6439 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.06 % Allowed : 1.40 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.18), residues: 1950 helix: -1.20 (0.14), residues: 1039 sheet: 0.50 (0.29), residues: 304 loop : 0.46 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.004 ARG F 212 TYR 0.039 0.005 TYR D 131 PHE 0.020 0.003 PHE C 25 HIS 0.010 0.003 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.25 (16603) covalent geometry : angle 0.77728 / 0.45 (22607) hydrogen bonds : bond 0.25940 / 17.29 ( 807) hydrogen bonds : angle 8.43706 / 5.95 ( 2273) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7304 (m-30) REVERT: B 295 GLU cc_start: 0.8089 (tt0) cc_final: 0.7832 (tt0) REVERT: C 90 LYS cc_start: 0.8236 (pttt) cc_final: 0.7952 (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: 0.7976 (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: 0.7566 (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: 0.8354 (p) REVERT: G 164 VAL cc_start: 0.8569 (t) cc_final: 0.8251 (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: 0.3765 time to fit residues: 213.7807 Evaluate side-chains 264 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN C 99 ASN D 166 ASN D 246 GLN F 255 HIS H 161 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.090241 restraints weight = 70796.496| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.31 r_work: 0.2898 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16603 Z= 0.166 Angle : 0.660 6.478 22607 Z= 0.354 Chirality : 0.043 0.164 2548 Planarity : 0.006 0.055 2808 Dihedral : 14.615 145.207 2626 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.91 % Allowed : 6.34 % Favored : 92.75 % 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: 0.14 (0.18), residues: 1950 helix: -0.05 (0.15), residues: 1079 sheet: 1.13 (0.31), residues: 271 loop : 0.21 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 48 TYR 0.019 0.001 TYR C 124 PHE 0.008 0.001 PHE B 307 HIS 0.008 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (16603) covalent geometry : angle 0.65995 / 0.35 (22607) hydrogen bonds : bond 0.07753 / 5.12 ( 807) hydrogen bonds : angle 5.94241 / 4.16 ( 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 289 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 274 time to evaluate : 0.805 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 76 MET cc_start: 0.9319 (mmm) cc_final: 0.9094 (mmt) REVERT: A 163 MET cc_start: 0.8963 (mmm) cc_final: 0.8729 (mmp) REVERT: A 291 ARG cc_start: 0.8043 (tpt-90) cc_final: 0.7815 (tpt-90) REVERT: A 296 ASP cc_start: 0.8109 (m-30) cc_final: 0.7882 (m-30) REVERT: B 295 GLU cc_start: 0.8748 (tt0) cc_final: 0.8504 (tt0) REVERT: C 90 LYS cc_start: 0.8145 (pttt) cc_final: 0.7861 (pttm) REVERT: C 105 ASP cc_start: 0.8445 (m-30) cc_final: 0.8221 (m-30) REVERT: C 325 MET cc_start: 0.9039 (mmp) cc_final: 0.8793 (mmp) REVERT: D 171 ARG cc_start: 0.8686 (mmt-90) cc_final: 0.8380 (mpt90) REVERT: D 309 MET cc_start: 0.9023 (mtp) cc_final: 0.8755 (mtp) REVERT: E 256 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7965 (mm-30) REVERT: E 272 MET cc_start: 0.8350 (mtt) cc_final: 0.8022 (mtt) REVERT: F 213 SER cc_start: 0.8852 (t) cc_final: 0.8635 (p) REVERT: F 295 GLU cc_start: 0.8483 (tt0) cc_final: 0.7919 (tt0) REVERT: G 203 LEU cc_start: 0.7096 (tp) cc_final: 0.6892 (tp) outliers start: 15 outliers final: 13 residues processed: 280 average time/residue: 0.3247 time to fit residues: 129.4724 Evaluate side-chains 272 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 259 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 287 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 324 HIS C 99 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 = 0.3406 r_free = 0.3406 target = 0.117337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090236 restraints weight = 69787.928| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.26 r_work: 0.2884 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16603 Z= 0.152 Angle : 0.586 6.228 22607 Z= 0.308 Chirality : 0.041 0.144 2548 Planarity : 0.005 0.051 2808 Dihedral : 14.309 137.799 2626 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.22 % Allowed : 7.13 % Favored : 91.65 % 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: 0.37 (0.19), residues: 1950 helix: 0.29 (0.16), residues: 1086 sheet: 0.92 (0.31), residues: 263 loop : 0.17 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 291 TYR 0.018 0.001 TYR C 124 PHE 0.008 0.001 PHE B 58 HIS 0.009 0.001 HIS H 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16603) covalent geometry : angle 0.58591 / 0.31 (22607) hydrogen bonds : bond 0.06514 / 4.27 ( 807) hydrogen bonds : angle 5.33507 / 3.74 ( 2273) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 0.840 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 76 MET cc_start: 0.9314 (mmm) cc_final: 0.9067 (mmt) REVERT: A 163 MET cc_start: 0.8957 (mmm) cc_final: 0.8739 (mmp) REVERT: A 291 ARG cc_start: 0.8028 (tpt-90) cc_final: 0.7766 (tpt-90) REVERT: A 296 ASP cc_start: 0.8045 (m-30) cc_final: 0.7807 (m-30) REVERT: B 242 LYS cc_start: 0.8810 (tppp) cc_final: 0.8454 (mmtt) REVERT: B 295 GLU cc_start: 0.8697 (tt0) cc_final: 0.8449 (tt0) REVERT: C 90 LYS cc_start: 0.8104 (pttt) cc_final: 0.7818 (pttm) REVERT: C 105 ASP cc_start: 0.8433 (m-30) cc_final: 0.8221 (m-30) REVERT: C 135 MET cc_start: 0.4476 (mmm) cc_final: 0.4023 (mmm) REVERT: C 325 MET cc_start: 0.8999 (mmp) cc_final: 0.8690 (mmp) REVERT: D 171 ARG cc_start: 0.8699 (mmt-90) cc_final: 0.8377 (mpt90) REVERT: D 309 MET cc_start: 0.9041 (mtp) cc_final: 0.8773 (mtp) REVERT: E 272 MET cc_start: 0.8364 (mtt) cc_final: 0.8053 (mtt) REVERT: F 211 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8422 (ttp-110) REVERT: F 213 SER cc_start: 0.8891 (t) cc_final: 0.8670 (p) REVERT: F 295 GLU cc_start: 0.8432 (tt0) cc_final: 0.7893 (tt0) REVERT: G 176 GLU cc_start: 0.8519 (tp30) cc_final: 0.8065 (tp30) REVERT: G 192 GLU cc_start: 0.7579 (tt0) cc_final: 0.7328 (mp0) REVERT: G 203 LEU cc_start: 0.6946 (tp) cc_final: 0.6695 (tp) outliers start: 20 outliers final: 14 residues processed: 272 average time/residue: 0.3241 time to fit residues: 124.9944 Evaluate side-chains 265 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 185 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 287 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 110 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.091013 restraints weight = 70357.263| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.22 r_work: 0.2869 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16603 Z= 0.122 Angle : 0.558 8.552 22607 Z= 0.289 Chirality : 0.040 0.174 2548 Planarity : 0.004 0.045 2808 Dihedral : 14.103 132.069 2626 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.16 % Allowed : 7.68 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1950 helix: 0.56 (0.16), residues: 1084 sheet: 1.06 (0.31), residues: 270 loop : 0.34 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 291 TYR 0.017 0.001 TYR C 124 PHE 0.010 0.001 PHE F 307 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16603) covalent geometry : angle 0.55751 / 0.29 (22607) hydrogen bonds : bond 0.05092 / 3.33 ( 807) hydrogen bonds : angle 5.01891 / 3.53 ( 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 275 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.914 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 296 ASP cc_start: 0.7991 (m-30) cc_final: 0.7746 (m-30) REVERT: A 297 MET cc_start: 0.8287 (tpp) cc_final: 0.7842 (ttp) REVERT: B 242 LYS cc_start: 0.8821 (tppp) cc_final: 0.8564 (mmtt) REVERT: B 295 GLU cc_start: 0.8677 (tt0) cc_final: 0.8445 (tt0) REVERT: C 90 LYS cc_start: 0.8101 (pttt) cc_final: 0.7816 (pttm) REVERT: C 105 ASP cc_start: 0.8475 (m-30) cc_final: 0.8273 (m-30) REVERT: C 135 MET cc_start: 0.4736 (mmm) cc_final: 0.4409 (mmm) REVERT: C 325 MET cc_start: 0.9016 (mmp) cc_final: 0.8665 (mmp) REVERT: D 21 ARG cc_start: 0.7592 (tpp80) cc_final: 0.7156 (mmm160) REVERT: D 171 ARG cc_start: 0.8669 (mmt-90) cc_final: 0.8375 (mpt90) REVERT: D 309 MET cc_start: 0.8961 (mtp) cc_final: 0.8672 (mtp) REVERT: E 110 ASP cc_start: 0.8986 (t0) cc_final: 0.8751 (t0) REVERT: E 256 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8281 (mm-30) REVERT: E 272 MET cc_start: 0.8311 (mtt) cc_final: 0.8008 (mtt) REVERT: F 295 GLU cc_start: 0.8548 (tt0) cc_final: 0.8011 (tt0) REVERT: G 176 GLU cc_start: 0.8379 (tp30) cc_final: 0.7963 (tp30) REVERT: G 180 MET cc_start: 0.7528 (mtm) cc_final: 0.7239 (mtm) REVERT: G 203 LEU cc_start: 0.6967 (tp) cc_final: 0.6733 (tp) outliers start: 19 outliers final: 15 residues processed: 265 average time/residue: 0.3282 time to fit residues: 123.7836 Evaluate side-chains 261 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 246 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 163 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain H residue 195 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 184 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 96 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 0.0010 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 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 = 0.3424 r_free = 0.3424 target = 0.118370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.091475 restraints weight = 71184.084| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.28 r_work: 0.2914 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16603 Z= 0.117 Angle : 0.539 6.094 22607 Z= 0.279 Chirality : 0.040 0.140 2548 Planarity : 0.004 0.040 2808 Dihedral : 13.963 127.181 2626 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.16 % Allowed : 8.78 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 1950 helix: 0.74 (0.16), residues: 1083 sheet: 1.09 (0.31), residues: 270 loop : 0.41 (0.25), residues: 597 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 B 58 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (16603) covalent geometry : angle 0.53933 / 0.28 (22607) hydrogen bonds : bond 0.04795 / 3.13 ( 807) hydrogen bonds : angle 4.87261 / 3.42 ( 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 272 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 0.790 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 296 ASP cc_start: 0.7964 (m-30) cc_final: 0.7742 (m-30) REVERT: C 90 LYS cc_start: 0.8082 (pttt) cc_final: 0.7807 (pttm) REVERT: C 105 ASP cc_start: 0.8422 (m-30) cc_final: 0.8221 (m-30) REVERT: C 325 MET cc_start: 0.8981 (mmp) cc_final: 0.8602 (mmp) REVERT: D 143 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7259 (mtm-85) REVERT: D 171 ARG cc_start: 0.8649 (mmt-90) cc_final: 0.8318 (mpt90) REVERT: D 309 MET cc_start: 0.8950 (mtp) cc_final: 0.8663 (mtp) REVERT: E 110 ASP cc_start: 0.9002 (t0) cc_final: 0.8764 (t0) REVERT: E 272 MET cc_start: 0.8300 (mtt) cc_final: 0.7994 (mtt) REVERT: F 211 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8448 (ttp-110) REVERT: F 272 MET cc_start: 0.8268 (mmp) cc_final: 0.7817 (mmm) REVERT: F 291 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7950 (ttm-80) REVERT: F 295 GLU cc_start: 0.8551 (tt0) cc_final: 0.8028 (tt0) REVERT: G 176 GLU cc_start: 0.8405 (tp30) cc_final: 0.7845 (tp30) REVERT: G 180 MET cc_start: 0.7468 (mtm) cc_final: 0.6849 (mtm) REVERT: G 203 LEU cc_start: 0.6935 (tp) cc_final: 0.6707 (tp) outliers start: 19 outliers final: 15 residues processed: 264 average time/residue: 0.3207 time to fit residues: 120.2704 Evaluate side-chains 265 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 249 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 121 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 211 ARG 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: 1.9990 chunk 52 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 170 optimal weight: 0.8980 chunk 189 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3404 r_free = 0.3404 target = 0.117284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090275 restraints weight = 69866.022| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.26 r_work: 0.2899 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3349 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= 0.140 Angle : 0.545 6.123 22607 Z= 0.281 Chirality : 0.040 0.172 2548 Planarity : 0.004 0.041 2808 Dihedral : 13.876 121.404 2626 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.34 % Allowed : 9.02 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 1950 helix: 0.85 (0.16), residues: 1083 sheet: 1.04 (0.31), residues: 270 loop : 0.33 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 291 TYR 0.017 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/Z covalent geometry : bond 0.00317 / 0.14 (16603) covalent geometry : angle 0.54515 / 0.28 (22607) hydrogen bonds : bond 0.04751 / 3.13 ( 807) hydrogen bonds : angle 4.77239 / 3.36 ( 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 271 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 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: A 105 ASP cc_start: 0.8695 (m-30) cc_final: 0.8489 (m-30) REVERT: A 296 ASP cc_start: 0.7986 (m-30) cc_final: 0.7765 (m-30) REVERT: A 297 MET cc_start: 0.8372 (tpp) cc_final: 0.7996 (ttp) REVERT: C 90 LYS cc_start: 0.8100 (pttt) cc_final: 0.7803 (pttm) REVERT: D 21 ARG cc_start: 0.7582 (tpp80) cc_final: 0.7142 (mmm160) REVERT: D 143 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7207 (mtm-85) REVERT: D 171 ARG cc_start: 0.8663 (mmt-90) cc_final: 0.8353 (mpt90) REVERT: D 309 MET cc_start: 0.8984 (mtp) cc_final: 0.8734 (mtp) REVERT: E 110 ASP cc_start: 0.9062 (t0) cc_final: 0.8845 (t0) REVERT: E 272 MET cc_start: 0.8351 (mtt) cc_final: 0.7940 (mtt) REVERT: F 267 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8230 (ttp-110) REVERT: F 295 GLU cc_start: 0.8435 (tt0) cc_final: 0.7918 (tt0) REVERT: G 176 GLU cc_start: 0.8388 (tp30) cc_final: 0.7849 (tp30) REVERT: G 180 MET cc_start: 0.7510 (mtm) cc_final: 0.6918 (mtm) REVERT: G 203 LEU cc_start: 0.6938 (tp) cc_final: 0.6717 (tp) outliers start: 22 outliers final: 17 residues processed: 263 average time/residue: 0.3432 time to fit residues: 128.6263 Evaluate side-chains 262 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 245 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 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 213 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN D 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.088862 restraints weight = 70298.416| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.25 r_work: 0.2862 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16603 Z= 0.195 Angle : 0.574 8.335 22607 Z= 0.297 Chirality : 0.041 0.131 2548 Planarity : 0.005 0.045 2808 Dihedral : 13.907 123.482 2626 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.40 % Allowed : 9.26 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1950 helix: 0.79 (0.16), residues: 1083 sheet: 0.92 (0.32), residues: 265 loop : 0.11 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.019 0.001 TYR C 124 PHE 0.009 0.001 PHE B 58 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (16603) covalent geometry : angle 0.57440 / 0.30 (22607) hydrogen bonds : bond 0.05256 / 3.48 ( 807) hydrogen bonds : angle 4.82404 / 3.40 ( 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 266 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8406 (tpp) cc_final: 0.8066 (ttp) REVERT: C 90 LYS cc_start: 0.8109 (pttt) cc_final: 0.7800 (pttm) REVERT: D 171 ARG cc_start: 0.8696 (mmt-90) cc_final: 0.8397 (mpt90) REVERT: D 309 MET cc_start: 0.9016 (mtp) cc_final: 0.8804 (mtp) REVERT: E 110 ASP cc_start: 0.9076 (t0) cc_final: 0.8862 (t0) REVERT: E 272 MET cc_start: 0.8422 (mtt) cc_final: 0.8010 (mtt) REVERT: F 105 ASP cc_start: 0.8516 (m-30) cc_final: 0.8293 (m-30) REVERT: F 267 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8251 (ttp-110) REVERT: F 295 GLU cc_start: 0.8426 (tt0) cc_final: 0.7919 (tt0) REVERT: G 203 LEU cc_start: 0.6955 (tp) cc_final: 0.6729 (tp) outliers start: 23 outliers final: 19 residues processed: 255 average time/residue: 0.3427 time to fit residues: 124.3318 Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 124 TYR 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 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 299 GLU Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 287 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 57 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.089811 restraints weight = 70098.746| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.24 r_work: 0.2827 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3516 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= 0.130 Angle : 0.552 8.167 22607 Z= 0.284 Chirality : 0.040 0.147 2548 Planarity : 0.004 0.045 2808 Dihedral : 13.830 127.167 2626 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.10 % Allowed : 9.69 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1950 helix: 0.92 (0.16), residues: 1083 sheet: 0.99 (0.32), residues: 262 loop : 0.13 (0.24), residues: 605 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 0.007 0.001 PHE B 58 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16603) covalent geometry : angle 0.55236 / 0.28 (22607) hydrogen bonds : bond 0.04662 / 3.08 ( 807) hydrogen bonds : angle 4.70775 / 3.32 ( 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 270 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 0.901 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: 0.8421 (tpp) cc_final: 0.8111 (ttp) REVERT: C 90 LYS cc_start: 0.8096 (pttt) cc_final: 0.7783 (pttm) REVERT: D 171 ARG cc_start: 0.8659 (mmt-90) cc_final: 0.8328 (mpt90) REVERT: D 309 MET cc_start: 0.8970 (mtp) cc_final: 0.8751 (mtp) REVERT: E 110 ASP cc_start: 0.9080 (t0) cc_final: 0.8873 (t0) REVERT: E 272 MET cc_start: 0.8426 (mtt) cc_final: 0.8046 (mtt) REVERT: F 105 ASP cc_start: 0.8506 (m-30) cc_final: 0.8272 (m-30) REVERT: F 211 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8519 (ttp-110) REVERT: F 267 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.8217 (ttp-110) REVERT: F 295 GLU cc_start: 0.8433 (tt0) cc_final: 0.7911 (tt0) REVERT: G 176 GLU cc_start: 0.8472 (tp30) cc_final: 0.7399 (tp30) REVERT: G 203 LEU cc_start: 0.7061 (tp) cc_final: 0.6827 (tp) outliers start: 18 outliers final: 16 residues processed: 264 average time/residue: 0.3515 time to fit residues: 132.0033 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 : 0.690 ------------------------------------------------------------------------------- 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 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 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=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: 0.8980 chunk 154 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 286 ASN B 79 ASN D 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.089363 restraints weight = 69531.696| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.19 r_work: 0.2884 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16603 Z= 0.170 Angle : 0.573 9.399 22607 Z= 0.296 Chirality : 0.040 0.131 2548 Planarity : 0.005 0.046 2808 Dihedral : 13.845 130.684 2626 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.04 % Allowed : 9.99 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1950 helix: 0.91 (0.16), residues: 1082 sheet: 0.94 (0.32), residues: 261 loop : 0.06 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 291 TYR 0.018 0.001 TYR C 124 PHE 0.008 0.001 PHE B 58 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (16603) covalent geometry : angle 0.57339 / 0.30 (22607) hydrogen bonds : bond 0.04926 / 3.26 ( 807) hydrogen bonds : angle 4.73196 / 3.34 ( 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 258 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8356 (tpp) cc_final: 0.8108 (ttp) REVERT: C 90 LYS cc_start: 0.8100 (pttt) cc_final: 0.7797 (pttm) REVERT: C 133 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7870 (p0) REVERT: C 135 MET cc_start: 0.4393 (mmm) cc_final: 0.4161 (mmm) REVERT: D 171 ARG cc_start: 0.8640 (mmt-90) cc_final: 0.8312 (mpt90) REVERT: D 309 MET cc_start: 0.8951 (mtp) cc_final: 0.8715 (mtp) REVERT: E 110 ASP cc_start: 0.9082 (t0) cc_final: 0.8871 (t0) REVERT: E 272 MET cc_start: 0.8374 (mtt) cc_final: 0.7978 (mtt) REVERT: F 105 ASP cc_start: 0.8503 (m-30) cc_final: 0.8295 (m-30) REVERT: F 267 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8240 (ttp-110) REVERT: F 272 MET cc_start: 0.8278 (mmp) cc_final: 0.7883 (mmm) REVERT: F 295 GLU cc_start: 0.8461 (tt0) cc_final: 0.7944 (tt0) REVERT: G 203 LEU cc_start: 0.7109 (tp) cc_final: 0.6886 (tp) outliers start: 17 outliers final: 15 residues processed: 253 average time/residue: 0.3413 time to fit residues: 122.4741 Evaluate side-chains 255 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 133 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 102 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 28 optimal weight: 0.0030 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.090491 restraints weight = 70052.446| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.25 r_work: 0.2870 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3654 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= 0.111 Angle : 0.544 7.850 22607 Z= 0.278 Chirality : 0.039 0.145 2548 Planarity : 0.004 0.042 2808 Dihedral : 13.750 129.052 2626 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.98 % Allowed : 9.93 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1950 helix: 1.09 (0.16), residues: 1081 sheet: 1.01 (0.32), residues: 261 loop : 0.19 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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/Z covalent geometry : bond 0.00244 / 0.11 (16603) covalent geometry : angle 0.54388 / 0.28 (22607) hydrogen bonds : bond 0.04237 / 2.79 ( 807) hydrogen bonds : angle 4.59944 / 3.25 ( 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 265 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 249 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 THR cc_start: 0.9385 (t) cc_final: 0.9039 (m) REVERT: A 297 MET cc_start: 0.8423 (tpp) cc_final: 0.8112 (ttp) REVERT: C 90 LYS cc_start: 0.8114 (pttt) cc_final: 0.7805 (pttm) REVERT: C 133 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7837 (p0) REVERT: C 135 MET cc_start: 0.4519 (mmm) cc_final: 0.3993 (mmm) REVERT: D 171 ARG cc_start: 0.8580 (mmt-90) cc_final: 0.8189 (mpt90) REVERT: D 309 MET cc_start: 0.8970 (mtp) cc_final: 0.8714 (mtp) REVERT: E 110 ASP cc_start: 0.9053 (t0) cc_final: 0.8839 (t0) REVERT: E 272 MET cc_start: 0.8384 (mtt) cc_final: 0.8016 (mtt) REVERT: F 105 ASP cc_start: 0.8548 (m-30) cc_final: 0.8306 (m-30) REVERT: F 267 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8171 (ttp-110) REVERT: F 272 MET cc_start: 0.8337 (mmp) cc_final: 0.7920 (mmm) REVERT: F 291 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7949 (ttm-80) REVERT: F 295 GLU cc_start: 0.8443 (tt0) cc_final: 0.7947 (tt0) REVERT: G 203 LEU cc_start: 0.7010 (tp) cc_final: 0.6760 (tp) outliers start: 16 outliers final: 14 residues processed: 259 average time/residue: 0.3439 time to fit residues: 127.2237 Evaluate side-chains 258 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 243 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 129 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.090562 restraints weight = 69603.861| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.20 r_work: 0.2904 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16603 Z= 0.128 Angle : 0.547 7.464 22607 Z= 0.279 Chirality : 0.039 0.149 2548 Planarity : 0.004 0.041 2808 Dihedral : 13.726 130.846 2626 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.91 % Allowed : 10.12 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.19), residues: 1950 helix: 1.13 (0.16), residues: 1082 sheet: 0.98 (0.32), residues: 261 loop : 0.16 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.016 0.001 TYR C 124 PHE 0.007 0.001 PHE B 58 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16603) covalent geometry : angle 0.54733 / 0.28 (22607) hydrogen bonds : bond 0.04282 / 2.83 ( 807) hydrogen bonds : angle 4.57423 / 3.23 ( 2273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7848.83 seconds wall clock time: 133 minutes 20.30 seconds (8000.30 seconds total)