Starting phenix.real_space_refine on Fri Mar 6 15:35:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbo_13297/03_2026/7pbo_13297_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbo_13297/03_2026/7pbo_13297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbo_13297/03_2026/7pbo_13297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbo_13297/03_2026/7pbo_13297.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbo_13297/03_2026/7pbo_13297_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbo_13297/03_2026/7pbo_13297_neut_trim.cif" } resolution = 2.9 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 2 5.21 5 S 100 5.16 5 C 10134 2.51 5 N 2757 2.21 5 O 3218 1.98 5 H 15818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32073 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 5.58, per 1000 atoms: 0.17 Number of scatterers: 32073 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 2 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: 2.72 Conformation dependent library (CDL) restraints added in 906.9 milliseconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 19 sheets defined 60.0% alpha, 10.6% beta 14 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.629A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.617A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (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: 3.578A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 130 removed outlier: 4.629A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.562A 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 197 removed outlier: 3.526A pdb=" N ILE A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.566A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 279 through 287 removed outlier: 3.661A pdb=" N ASN A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.615A 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 49 Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.545A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.651A 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 121 Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.887A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.506A pdb=" N ILE B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 216 through 235 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.605A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.599A 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: 3.629A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.613A 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: 4.001A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.762A 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: 3.648A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 202 through 212 removed outlier: 3.546A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 234 removed outlier: 3.552A pdb=" N ILE C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 259 through 273 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: 3.874A pdb=" N LEU C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.552A pdb=" N TYR C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.712A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 77 removed outlier: 3.597A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.696A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 116 through 130 removed outlier: 4.459A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.627A 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 170 Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.621A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 removed outlier: 3.767A pdb=" N GLU D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 234 Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.635A pdb=" N GLY D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 removed outlier: 3.691A 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: 3.633A 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 49 removed outlier: 3.909A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.629A 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: 3.701A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.895A 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 129 removed outlier: 3.695A pdb=" N GLU E 120 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 removed outlier: 3.600A pdb=" N ALA E 170 " --> pdb=" O ASN E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 202 through 212 Processing helix chain 'E' and resid 216 through 235 removed outlier: 3.728A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 252 Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.553A pdb=" N LEU E 266 " --> pdb=" O ASP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 287 Processing helix chain 'E' and resid 290 through 298 removed outlier: 3.604A pdb=" N ASP E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 removed outlier: 3.613A pdb=" N LEU E 302 " --> pdb=" O TYR E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 removed outlier: 3.513A pdb=" N TYR E 322 " --> pdb=" O THR E 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 48 removed outlier: 4.007A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.666A 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: 3.519A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.332A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 216 through 235 removed outlier: 3.548A pdb=" N ASP F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 251 removed outlier: 3.717A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.688A pdb=" N LYS F 264 " --> pdb=" O TYR F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.566A 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: 3.712A pdb=" N ILE H 184 " --> pdb=" O MET H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 203 removed outlier: 3.931A pdb=" N ARG H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.555A pdb=" N LYS A 81 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASP A 110 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR A 83 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 136 removed outlier: 3.598A pdb=" N ILE A 136 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 143 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 removed outlier: 6.991A 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: 6.494A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 56 " --> pdb=" O GLY B 176 " (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: 6.417A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU C 56 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.574A pdb=" N LYS D 81 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASP D 110 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR D 83 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR D 55 " --> pdb=" O GLY D 156 " (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: 6.652A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (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 308 through 311 Processing sheet with id=AB8, first strand: chain 'F' and resid 80 through 84 removed outlier: 3.575A pdb=" N ASP F 110 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU F 56 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AC1, first strand: chain 'F' and resid 308 through 310 779 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 7.67 Time building geometry restraints manager: 3.69 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: 6909 1.50 - 1.72: 6775 1.72 - 1.94: 198 Bond restraints: 32421 Sorted by residual: bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR A 19 " pdb=" H1 THR A 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+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 2.50e+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 2.50e+01 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 2.49e+01 ... (remaining 32416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 57921 1.99 - 3.98: 685 3.98 - 5.97: 58 5.97 - 7.96: 13 7.96 - 9.95: 7 Bond angle restraints: 58684 Sorted by residual: angle pdb=" N GLY E 215 " pdb=" CA GLY E 215 " pdb=" C GLY E 215 " ideal model delta sigma weight residual 115.32 120.27 -4.95 1.38e+00 5.25e-01 1.29e+01 angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 110.05 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA TYR C 124 " pdb=" CB TYR C 124 " pdb=" CG TYR C 124 " ideal model delta sigma weight residual 113.90 119.43 -5.53 1.80e+00 3.09e-01 9.43e+00 angle pdb=" C2' ADP E 600 " pdb=" C3' ADP E 600 " pdb=" C4' ADP E 600 " ideal model delta sigma weight residual 111.00 101.97 9.03 3.00e+00 1.11e-01 9.07e+00 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 116.94 -8.94 3.00e+00 1.11e-01 8.88e+00 ... (remaining 58679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.46: 14433 31.46 - 62.92: 557 62.92 - 94.38: 34 94.38 - 125.84: 0 125.84 - 157.30: 6 Dihedral angle restraints: 15030 sinusoidal: 8597 harmonic: 6433 Sorted by residual: dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 97.30 -157.30 1 2.00e+01 2.50e-03 4.61e+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 87.04 -147.04 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O2A ADP A 600 " pdb=" O3A ADP A 600 " pdb=" PA ADP A 600 " pdb=" PB ADP A 600 " ideal model delta sinusoidal sigma weight residual -60.00 78.45 -138.44 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 15027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2276 0.073 - 0.146: 269 0.146 - 0.219: 6 0.219 - 0.293: 0 0.293 - 0.366: 1 Chirality restraints: 2552 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.71 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA PHE D 197 " pdb=" N PHE D 197 " pdb=" C PHE D 197 " pdb=" CB PHE D 197 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA ARG E 214 " pdb=" N ARG E 214 " pdb=" C ARG E 214 " pdb=" CB ARG E 214 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 2549 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 218 " 0.089 9.50e-02 1.11e+02 5.16e-02 4.08e+01 pdb=" NE ARG F 218 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG F 218 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG F 218 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 218 " -0.080 2.00e-02 2.50e+03 pdb="HH11 ARG F 218 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 218 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG F 218 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG F 218 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.041 2.00e-02 2.50e+03 5.12e-02 3.94e+01 pdb=" CD GLN C 31 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.082 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.002 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 48 " -0.028 9.50e-02 1.11e+02 3.64e-02 2.79e+01 pdb=" NE ARG B 48 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 48 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG B 48 " -0.062 2.00e-02 2.50e+03 pdb=" NH2 ARG B 48 " 0.024 2.00e-02 2.50e+03 pdb="HH11 ARG B 48 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 48 " 0.066 2.00e-02 2.50e+03 pdb="HH21 ARG B 48 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 48 " -0.024 2.00e-02 2.50e+03 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 814 2.14 - 2.76: 58097 2.76 - 3.37: 84153 3.37 - 3.99: 108274 3.99 - 4.60: 173968 Nonbonded interactions: 425306 Sorted by model distance: nonbonded pdb=" HG1 THR F 66 " pdb=" O1B ADP F 600 " model vdw 1.528 2.450 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.552 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.556 2.450 nonbonded pdb=" O LEU E 52 " pdb=" HG1 THR E 153 " model vdw 1.573 2.450 nonbonded pdb=" HZ1 LYS F 264 " pdb=" O ILE F 287 " model vdw 1.583 2.450 ... (remaining 425301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } ncs_group { reference = (chain 'G' and (resid 158 through 202 or (resid 203 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name H or name H \ A or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or n \ ame HD21 or name HD22 or name HD23)))) selection = (chain 'H' and resid 158 through 203) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.180 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.730 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16603 Z= 0.182 Angle : 0.741 9.946 22607 Z= 0.421 Chirality : 0.045 0.366 2552 Planarity : 0.010 0.133 2808 Dihedral : 14.888 157.300 6403 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.12 % Allowed : 1.34 % 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: -0.74 (0.18), residues: 1950 helix: -1.07 (0.14), residues: 1030 sheet: 0.36 (0.29), residues: 313 loop : 0.58 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.004 ARG H 200 TYR 0.041 0.006 TYR C 131 PHE 0.020 0.003 PHE C 25 HIS 0.013 0.003 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00418 (16603) covalent geometry : angle 0.74054 (22607) hydrogen bonds : bond 0.27203 ( 812) hydrogen bonds : angle 8.52041 ( 2298) *********************** 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 517 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 515 time to evaluate : 0.773 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: 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: 0.8960 (tpp) cc_final: 0.8637 (tpp) REVERT: A 76 MET cc_start: 0.8264 (mmm) cc_final: 0.8026 (mmt) REVERT: A 144 SER cc_start: 0.8511 (p) cc_final: 0.8021 (t) REVERT: B 185 ASP cc_start: 0.7653 (m-30) cc_final: 0.7385 (m-30) REVERT: B 252 ASP cc_start: 0.7857 (t0) cc_final: 0.7422 (t0) REVERT: B 262 ASP cc_start: 0.8003 (m-30) cc_final: 0.7667 (m-30) REVERT: C 76 MET cc_start: 0.8626 (mmm) cc_final: 0.8365 (mmm) REVERT: C 124 TYR cc_start: 0.8311 (p90) cc_final: 0.8081 (p90) REVERT: C 130 TYR cc_start: 0.8880 (m-80) cc_final: 0.8680 (m-80) REVERT: C 199 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7572 (mmm) REVERT: C 296 ASP cc_start: 0.7365 (m-30) cc_final: 0.7133 (m-30) REVERT: D 76 MET cc_start: 0.8612 (mmm) cc_final: 0.8407 (mmm) REVERT: D 131 TYR cc_start: 0.8610 (p90) cc_final: 0.8223 (p90) REVERT: D 262 ASP cc_start: 0.7886 (m-30) cc_final: 0.7597 (m-30) REVERT: D 311 THR cc_start: 0.8680 (m) cc_final: 0.8472 (p) REVERT: D 313 THR cc_start: 0.8853 (m) cc_final: 0.8589 (p) REVERT: E 39 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7119 (mtmt) REVERT: E 42 ILE cc_start: 0.8924 (mt) cc_final: 0.8719 (mm) REVERT: E 79 ASN cc_start: 0.7708 (m-40) cc_final: 0.7157 (m110) REVERT: E 99 ASN cc_start: 0.7284 (t0) cc_final: 0.7072 (t0) REVERT: E 110 ASP cc_start: 0.7263 (t0) cc_final: 0.6945 (t0) REVERT: E 252 ASP cc_start: 0.7696 (t0) cc_final: 0.7462 (t0) REVERT: E 289 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6378 (mm-30) REVERT: E 325 MET cc_start: 0.8783 (mmm) cc_final: 0.8472 (mmp) REVERT: F 110 ASP cc_start: 0.7591 (t0) cc_final: 0.6708 (t70) REVERT: F 119 VAL cc_start: 0.7516 (t) cc_final: 0.7159 (t) REVERT: F 253 VAL cc_start: 0.8541 (t) cc_final: 0.8326 (p) REVERT: F 259 ASP cc_start: 0.7045 (t0) cc_final: 0.6717 (t70) outliers start: 2 outliers final: 1 residues processed: 516 average time/residue: 1.7029 time to fit residues: 949.5347 Evaluate side-chains 403 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 401 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain F residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0470 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 79 ASN C 166 ASN C 286 ASN D 146 HIS D 166 ASN D 221 ASN D 286 ASN F 255 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.089208 restraints weight = 69130.757| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.32 r_work: 0.2970 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16603 Z= 0.177 Angle : 0.680 7.279 22607 Z= 0.363 Chirality : 0.042 0.140 2552 Planarity : 0.006 0.066 2808 Dihedral : 14.422 145.320 2593 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.86 % Allowed : 13.95 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 1950 helix: 0.28 (0.15), residues: 1057 sheet: 0.55 (0.30), residues: 286 loop : 0.52 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 196 TYR 0.024 0.001 TYR C 124 PHE 0.012 0.001 PHE E 70 HIS 0.009 0.001 HIS F 255 Details of bonding type rmsd covalent geometry : bond 0.00379 (16603) covalent geometry : angle 0.67959 (22607) hydrogen bonds : bond 0.08197 ( 812) hydrogen bonds : angle 5.86830 ( 2298) *********************** 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 457 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 410 time to evaluate : 0.640 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9280 (tpp) cc_final: 0.8909 (tpp) REVERT: A 144 SER cc_start: 0.8604 (p) cc_final: 0.7946 (t) REVERT: A 240 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: A 292 GLU cc_start: 0.7617 (mp0) cc_final: 0.7235 (mp0) REVERT: A 295 GLU cc_start: 0.7706 (tp30) cc_final: 0.7216 (tp30) REVERT: B 147 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 185 ASP cc_start: 0.8299 (m-30) cc_final: 0.8035 (m-30) REVERT: B 252 ASP cc_start: 0.8506 (t0) cc_final: 0.8089 (t0) REVERT: C 117 MET cc_start: 0.6992 (tpp) cc_final: 0.6132 (tpp) REVERT: C 121 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: C 124 TYR cc_start: 0.8616 (p90) cc_final: 0.8319 (p90) REVERT: C 199 MET cc_start: 0.8368 (mmt) cc_final: 0.8143 (mmm) REVERT: D 90 LYS cc_start: 0.8539 (ptmm) cc_final: 0.8164 (ptpt) REVERT: D 120 GLU cc_start: 0.7878 (tt0) cc_final: 0.7399 (tt0) REVERT: D 171 ARG cc_start: 0.9021 (mmt90) cc_final: 0.8451 (mpt-90) REVERT: D 197 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.5415 (p90) REVERT: D 242 LYS cc_start: 0.8340 (tppt) cc_final: 0.8094 (tppt) REVERT: D 262 ASP cc_start: 0.8418 (m-30) cc_final: 0.8148 (m-30) REVERT: D 311 THR cc_start: 0.8610 (m) cc_final: 0.8282 (p) REVERT: D 313 THR cc_start: 0.8752 (m) cc_final: 0.8509 (p) REVERT: E 39 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7961 (mtmt) REVERT: E 43 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: E 110 ASP cc_start: 0.8033 (t0) cc_final: 0.7657 (t0) REVERT: E 135 MET cc_start: 0.6315 (mtm) cc_final: 0.6108 (mtm) REVERT: E 289 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7133 (mm-30) REVERT: E 291 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7416 (ptm-80) REVERT: F 81 LYS cc_start: 0.8299 (mttt) cc_final: 0.7909 (tptp) REVERT: F 109 ILE cc_start: 0.8893 (mt) cc_final: 0.8666 (mm) REVERT: F 110 ASP cc_start: 0.8037 (t0) cc_final: 0.7819 (t0) REVERT: F 204 GLU cc_start: 0.7579 (tp30) cc_final: 0.7270 (tp30) REVERT: F 253 VAL cc_start: 0.8794 (t) cc_final: 0.8500 (p) REVERT: F 297 MET cc_start: 0.7192 (tpp) cc_final: 0.6864 (tpp) REVERT: F 299 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: F 309 MET cc_start: 0.4789 (mmm) cc_final: 0.4561 (mmm) REVERT: G 179 ARG cc_start: 0.7827 (ttt-90) cc_final: 0.7592 (ttt-90) outliers start: 47 outliers final: 15 residues processed: 431 average time/residue: 1.6430 time to fit residues: 765.8886 Evaluate side-chains 413 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 391 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 99 ASN C 79 ASN C 166 ASN D 99 ASN D 146 HIS D 166 ASN D 221 ASN E 23 GLN F 246 GLN ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.088030 restraints weight = 69564.888| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.31 r_work: 0.2937 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3476 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= 0.179 Angle : 0.634 6.818 22607 Z= 0.332 Chirality : 0.041 0.152 2552 Planarity : 0.005 0.050 2808 Dihedral : 14.411 151.022 2590 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.62 % Allowed : 16.27 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 1950 helix: 0.62 (0.16), residues: 1058 sheet: 0.62 (0.30), residues: 274 loop : 0.21 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 310 TYR 0.021 0.001 TYR C 124 PHE 0.013 0.001 PHE D 197 HIS 0.033 0.002 HIS F 255 Details of bonding type rmsd covalent geometry : bond 0.00400 (16603) covalent geometry : angle 0.63424 (22607) hydrogen bonds : bond 0.06655 ( 812) hydrogen bonds : angle 5.27810 ( 2298) *********************** 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 439 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 396 time to evaluate : 0.786 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9251 (tpp) cc_final: 0.8927 (tpp) REVERT: A 144 SER cc_start: 0.8614 (p) cc_final: 0.7972 (t) REVERT: A 240 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: A 295 GLU cc_start: 0.7762 (tp30) cc_final: 0.7498 (tp30) REVERT: B 147 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8140 (mt) REVERT: B 185 ASP cc_start: 0.8312 (m-30) cc_final: 0.8079 (m-30) REVERT: B 252 ASP cc_start: 0.8491 (t0) cc_final: 0.8104 (t0) REVERT: B 291 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7786 (mtp85) REVERT: C 53 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7880 (t0) REVERT: C 81 LYS cc_start: 0.8312 (mmtm) cc_final: 0.8030 (mmmm) REVERT: C 89 GLU cc_start: 0.7373 (mp0) cc_final: 0.7081 (mm-30) REVERT: C 117 MET cc_start: 0.6615 (tpp) cc_final: 0.5904 (tpp) REVERT: C 121 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: C 199 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8205 (mmm) REVERT: D 90 LYS cc_start: 0.8372 (ptmm) cc_final: 0.8117 (ptpt) REVERT: D 105 ASP cc_start: 0.8399 (m-30) cc_final: 0.8080 (m-30) REVERT: D 120 GLU cc_start: 0.7748 (tt0) cc_final: 0.7297 (tt0) REVERT: D 131 TYR cc_start: 0.8619 (p90) cc_final: 0.8298 (p90) REVERT: D 171 ARG cc_start: 0.8991 (mmt90) cc_final: 0.8476 (mpt-90) REVERT: D 179 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6885 (pp20) REVERT: D 197 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.5535 (p90) REVERT: D 262 ASP cc_start: 0.8379 (m-30) cc_final: 0.8119 (m-30) REVERT: D 311 THR cc_start: 0.8529 (m) cc_final: 0.8260 (p) REVERT: D 313 THR cc_start: 0.8909 (m) cc_final: 0.8635 (p) REVERT: E 43 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: E 68 MET cc_start: 0.8675 (tpp) cc_final: 0.8475 (tpt) REVERT: E 110 ASP cc_start: 0.8097 (t0) cc_final: 0.7730 (t0) REVERT: E 129 ASP cc_start: 0.7521 (t0) cc_final: 0.6805 (t0) REVERT: E 131 TYR cc_start: 0.7717 (p90) cc_final: 0.6914 (p90) REVERT: E 135 MET cc_start: 0.6353 (mtm) cc_final: 0.6152 (ttm) REVERT: E 242 LYS cc_start: 0.8151 (mmmm) cc_final: 0.7927 (mttm) REVERT: E 289 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7179 (mm-30) REVERT: F 209 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7944 (tp) REVERT: F 255 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7852 (t-90) REVERT: F 280 LEU cc_start: 0.4680 (OUTLIER) cc_final: 0.4432 (tp) REVERT: F 297 MET cc_start: 0.7076 (tpp) cc_final: 0.6755 (tpp) REVERT: F 299 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: F 309 MET cc_start: 0.4808 (mmm) cc_final: 0.4588 (mmm) REVERT: G 162 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6750 (mt-10) REVERT: G 179 ARG cc_start: 0.7899 (ttt-90) cc_final: 0.7541 (ttt-90) outliers start: 43 outliers final: 15 residues processed: 411 average time/residue: 1.6197 time to fit residues: 721.4823 Evaluate side-chains 411 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 384 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 89 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 173 optimal weight: 0.3980 chunk 110 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS C 79 ASN D 99 ASN D 146 HIS D 286 ASN E 23 GLN F 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.089122 restraints weight = 68668.401| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.26 r_work: 0.2966 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16603 Z= 0.152 Angle : 0.619 7.442 22607 Z= 0.319 Chirality : 0.040 0.128 2552 Planarity : 0.005 0.058 2808 Dihedral : 14.335 153.130 2588 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.74 % Allowed : 17.06 % Favored : 80.20 % 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: 0.75 (0.19), residues: 1950 helix: 0.81 (0.16), residues: 1059 sheet: 0.57 (0.30), residues: 278 loop : 0.16 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 196 TYR 0.019 0.001 TYR C 124 PHE 0.013 0.001 PHE D 197 HIS 0.032 0.001 HIS F 255 Details of bonding type rmsd covalent geometry : bond 0.00338 (16603) covalent geometry : angle 0.61930 (22607) hydrogen bonds : bond 0.05673 ( 812) hydrogen bonds : angle 5.04838 ( 2298) *********************** 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 439 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 394 time to evaluate : 0.819 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9224 (tpp) cc_final: 0.8900 (tpp) REVERT: A 144 SER cc_start: 0.8600 (p) cc_final: 0.7964 (t) REVERT: A 295 GLU cc_start: 0.7768 (tp30) cc_final: 0.7520 (tp30) REVERT: B 147 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8085 (mt) REVERT: B 185 ASP cc_start: 0.8299 (m-30) cc_final: 0.8074 (m-30) REVERT: B 252 ASP cc_start: 0.8482 (t0) cc_final: 0.8086 (t0) REVERT: B 291 ARG cc_start: 0.7978 (mtp85) cc_final: 0.7704 (mtp85) REVERT: C 89 GLU cc_start: 0.7433 (mp0) cc_final: 0.7138 (mm-30) REVERT: C 117 MET cc_start: 0.6574 (tpp) cc_final: 0.5743 (tpp) REVERT: C 121 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: C 211 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8404 (mtt-85) REVERT: D 105 ASP cc_start: 0.8420 (m-30) cc_final: 0.8059 (m-30) REVERT: D 120 GLU cc_start: 0.7716 (tt0) cc_final: 0.7469 (tt0) REVERT: D 171 ARG cc_start: 0.8956 (mmt90) cc_final: 0.8492 (mpt-90) REVERT: D 179 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6935 (pp20) REVERT: D 197 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.5631 (p90) REVERT: D 262 ASP cc_start: 0.8352 (m-30) cc_final: 0.8086 (m-30) REVERT: D 311 THR cc_start: 0.8456 (m) cc_final: 0.8188 (p) REVERT: E 110 ASP cc_start: 0.8103 (t0) cc_final: 0.7728 (t0) REVERT: E 129 ASP cc_start: 0.7592 (t0) cc_final: 0.6878 (t0) REVERT: E 135 MET cc_start: 0.6329 (mtm) cc_final: 0.6102 (ttm) REVERT: E 289 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7109 (mm-30) REVERT: F 209 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7841 (tp) REVERT: F 269 MET cc_start: 0.7078 (mtp) cc_final: 0.6595 (tmm) REVERT: F 280 LEU cc_start: 0.4736 (OUTLIER) cc_final: 0.4520 (tp) REVERT: F 297 MET cc_start: 0.7004 (tpp) cc_final: 0.6705 (tpp) REVERT: F 299 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: F 309 MET cc_start: 0.4795 (mmm) cc_final: 0.4576 (mmm) REVERT: G 162 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6789 (mt-10) REVERT: G 179 ARG cc_start: 0.7926 (ttt-90) cc_final: 0.7536 (ttt-90) outliers start: 45 outliers final: 16 residues processed: 412 average time/residue: 1.6206 time to fit residues: 724.5561 Evaluate side-chains 406 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 382 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 169 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN D 146 HIS D 286 ASN E 23 GLN F 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.088113 restraints weight = 69276.729| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.29 r_work: 0.2942 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16603 Z= 0.169 Angle : 0.618 6.683 22607 Z= 0.318 Chirality : 0.041 0.132 2552 Planarity : 0.005 0.062 2808 Dihedral : 14.321 157.598 2588 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.62 % Allowed : 18.10 % Favored : 79.28 % 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: 0.73 (0.19), residues: 1950 helix: 0.86 (0.16), residues: 1059 sheet: 0.52 (0.30), residues: 276 loop : 0.03 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 310 TYR 0.018 0.001 TYR C 124 PHE 0.014 0.001 PHE D 197 HIS 0.007 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00389 (16603) covalent geometry : angle 0.61802 (22607) hydrogen bonds : bond 0.05565 ( 812) hydrogen bonds : angle 4.91913 ( 2298) *********************** 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 428 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 385 time to evaluate : 0.870 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9202 (tpp) cc_final: 0.8891 (tpp) REVERT: A 144 SER cc_start: 0.8607 (p) cc_final: 0.7981 (t) REVERT: A 240 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: A 295 GLU cc_start: 0.7772 (tp30) cc_final: 0.7550 (tp30) REVERT: B 185 ASP cc_start: 0.8306 (m-30) cc_final: 0.8101 (m-30) REVERT: B 252 ASP cc_start: 0.8490 (t0) cc_final: 0.8091 (t0) REVERT: B 291 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7661 (mtp85) REVERT: C 81 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8066 (mmtm) REVERT: C 89 GLU cc_start: 0.7411 (mp0) cc_final: 0.7111 (mm-30) REVERT: C 117 MET cc_start: 0.6494 (tpp) cc_final: 0.5644 (tpp) REVERT: C 121 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: C 182 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7524 (mm-30) REVERT: C 211 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8522 (mtt-85) REVERT: D 81 LYS cc_start: 0.8247 (mtmt) cc_final: 0.8023 (mmtp) REVERT: D 105 ASP cc_start: 0.8311 (m-30) cc_final: 0.8009 (m-30) REVERT: D 171 ARG cc_start: 0.8967 (mmt90) cc_final: 0.8492 (mpt-90) REVERT: D 179 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7173 (pp20) REVERT: D 197 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.5693 (p90) REVERT: D 262 ASP cc_start: 0.8384 (m-30) cc_final: 0.8136 (m-30) REVERT: D 311 THR cc_start: 0.8433 (m) cc_final: 0.8166 (p) REVERT: E 68 MET cc_start: 0.8690 (tpp) cc_final: 0.8190 (tpt) REVERT: E 110 ASP cc_start: 0.8112 (t0) cc_final: 0.7742 (t0) REVERT: E 129 ASP cc_start: 0.7507 (t0) cc_final: 0.7017 (t0) REVERT: E 135 MET cc_start: 0.6352 (mtm) cc_final: 0.6116 (ttm) REVERT: E 289 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7114 (mm-30) REVERT: F 209 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7808 (tp) REVERT: F 269 MET cc_start: 0.7116 (mtp) cc_final: 0.6661 (tmm) REVERT: F 280 LEU cc_start: 0.4740 (OUTLIER) cc_final: 0.4529 (tp) REVERT: F 297 MET cc_start: 0.7017 (tpp) cc_final: 0.6728 (tpp) REVERT: F 299 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: F 309 MET cc_start: 0.4798 (mmm) cc_final: 0.4572 (mmm) REVERT: G 162 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6821 (mt-10) REVERT: G 179 ARG cc_start: 0.8013 (ttt-90) cc_final: 0.7542 (ttt-90) outliers start: 43 outliers final: 18 residues processed: 402 average time/residue: 1.6644 time to fit residues: 726.6092 Evaluate side-chains 406 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 380 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 1 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 162 optimal weight: 0.0770 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN D 82 GLN D 146 HIS D 286 ASN E 23 GLN E 99 ASN F 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088701 restraints weight = 69150.119| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.27 r_work: 0.2966 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16603 Z= 0.151 Angle : 0.614 8.710 22607 Z= 0.314 Chirality : 0.040 0.130 2552 Planarity : 0.005 0.070 2808 Dihedral : 14.264 157.853 2588 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.44 % Allowed : 18.95 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 1950 helix: 0.95 (0.16), residues: 1060 sheet: 0.52 (0.30), residues: 276 loop : 0.02 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 196 TYR 0.019 0.001 TYR D 131 PHE 0.014 0.001 PHE D 197 HIS 0.007 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00345 (16603) covalent geometry : angle 0.61444 (22607) hydrogen bonds : bond 0.05155 ( 812) hydrogen bonds : angle 4.80252 ( 2298) *********************** 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 421 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 381 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9178 (tpp) cc_final: 0.8869 (tpp) REVERT: A 144 SER cc_start: 0.8629 (p) cc_final: 0.7970 (t) REVERT: A 240 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7570 (m-30) REVERT: A 295 GLU cc_start: 0.7767 (tp30) cc_final: 0.7563 (tp30) REVERT: B 185 ASP cc_start: 0.8293 (m-30) cc_final: 0.8089 (m-30) REVERT: B 252 ASP cc_start: 0.8479 (t0) cc_final: 0.8076 (t0) REVERT: B 291 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7638 (mtp85) REVERT: C 81 LYS cc_start: 0.8379 (mmtm) cc_final: 0.8091 (mmtm) REVERT: C 89 GLU cc_start: 0.7397 (mp0) cc_final: 0.7106 (mm-30) REVERT: C 117 MET cc_start: 0.6447 (tpp) cc_final: 0.5542 (tpp) REVERT: C 121 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: C 182 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7414 (mm-30) REVERT: C 211 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8500 (mtt-85) REVERT: D 105 ASP cc_start: 0.8308 (m-30) cc_final: 0.7958 (m-30) REVERT: D 171 ARG cc_start: 0.8913 (mmt90) cc_final: 0.8515 (mpt-90) REVERT: D 179 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7204 (pp20) REVERT: D 197 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.5725 (p90) REVERT: D 262 ASP cc_start: 0.8358 (m-30) cc_final: 0.8113 (m-30) REVERT: D 292 GLU cc_start: 0.8311 (pm20) cc_final: 0.8077 (pm20) REVERT: E 68 MET cc_start: 0.8680 (tpp) cc_final: 0.8193 (tpt) REVERT: E 110 ASP cc_start: 0.8104 (t0) cc_final: 0.7329 (t0) REVERT: E 111 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7617 (mt-10) REVERT: E 129 ASP cc_start: 0.7511 (t0) cc_final: 0.7121 (t0) REVERT: E 135 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.6174 (ttm) REVERT: E 289 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7118 (mm-30) REVERT: E 295 GLU cc_start: 0.8324 (tt0) cc_final: 0.7906 (tm-30) REVERT: F 105 ASP cc_start: 0.7937 (m-30) cc_final: 0.7626 (m-30) REVERT: F 115 MET cc_start: 0.6528 (tpp) cc_final: 0.6306 (tpp) REVERT: F 204 GLU cc_start: 0.7510 (tp30) cc_final: 0.7270 (tp30) REVERT: F 269 MET cc_start: 0.7051 (mtp) cc_final: 0.6584 (tmm) REVERT: F 280 LEU cc_start: 0.4742 (OUTLIER) cc_final: 0.4522 (tp) REVERT: F 297 MET cc_start: 0.7042 (tpp) cc_final: 0.6743 (tpp) REVERT: F 299 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: F 309 MET cc_start: 0.4817 (mmm) cc_final: 0.4597 (mmm) REVERT: G 162 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6871 (mt-10) REVERT: G 179 ARG cc_start: 0.7998 (ttt-90) cc_final: 0.7549 (ttt-90) outliers start: 40 outliers final: 18 residues processed: 397 average time/residue: 1.6829 time to fit residues: 724.1588 Evaluate side-chains 396 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 370 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 121 optimal weight: 0.0980 chunk 113 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN D 82 GLN D 146 HIS D 286 ASN E 23 GLN F 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.088573 restraints weight = 69518.281| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.28 r_work: 0.2963 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16603 Z= 0.155 Angle : 0.615 8.949 22607 Z= 0.313 Chirality : 0.040 0.131 2552 Planarity : 0.005 0.071 2808 Dihedral : 14.231 158.371 2588 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.44 % Allowed : 19.26 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 1950 helix: 1.00 (0.16), residues: 1061 sheet: 0.52 (0.30), residues: 276 loop : 0.01 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 310 TYR 0.017 0.001 TYR C 124 PHE 0.014 0.001 PHE D 197 HIS 0.008 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00359 (16603) covalent geometry : angle 0.61468 (22607) hydrogen bonds : bond 0.05058 ( 812) hydrogen bonds : angle 4.74435 ( 2298) *********************** 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 416 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 376 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9186 (tpp) cc_final: 0.8886 (tpp) REVERT: A 144 SER cc_start: 0.8606 (p) cc_final: 0.7953 (t) REVERT: A 240 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: B 101 LEU cc_start: 0.8917 (mt) cc_final: 0.8692 (mp) REVERT: B 185 ASP cc_start: 0.8287 (m-30) cc_final: 0.8086 (m-30) REVERT: B 252 ASP cc_start: 0.8468 (t0) cc_final: 0.8091 (t0) REVERT: B 291 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7628 (mtp85) REVERT: C 81 LYS cc_start: 0.8391 (mmtm) cc_final: 0.8108 (mmtm) REVERT: C 89 GLU cc_start: 0.7430 (mp0) cc_final: 0.7140 (mm-30) REVERT: C 117 MET cc_start: 0.6513 (tpp) cc_final: 0.6128 (mmm) REVERT: C 182 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7423 (mm-30) REVERT: C 211 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8499 (mtt-85) REVERT: D 105 ASP cc_start: 0.8333 (m-30) cc_final: 0.7996 (m-30) REVERT: D 179 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7192 (pp20) REVERT: D 197 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.5679 (p90) REVERT: D 262 ASP cc_start: 0.8371 (m-30) cc_final: 0.8119 (m-30) REVERT: D 292 GLU cc_start: 0.8349 (pm20) cc_final: 0.8093 (pm20) REVERT: E 68 MET cc_start: 0.8694 (tpp) cc_final: 0.8213 (tpt) REVERT: E 110 ASP cc_start: 0.8097 (t0) cc_final: 0.7294 (t0) REVERT: E 111 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7596 (mt-10) REVERT: E 129 ASP cc_start: 0.7560 (t0) cc_final: 0.7131 (t0) REVERT: E 135 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.6186 (ttm) REVERT: E 289 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7088 (mm-30) REVERT: E 310 ARG cc_start: 0.7176 (ttm110) cc_final: 0.6917 (mtm180) REVERT: F 105 ASP cc_start: 0.7927 (m-30) cc_final: 0.7636 (m-30) REVERT: F 115 MET cc_start: 0.6573 (tpp) cc_final: 0.6329 (tpp) REVERT: F 199 MET cc_start: 0.7636 (tpp) cc_final: 0.7417 (tpp) REVERT: F 269 MET cc_start: 0.7098 (mtp) cc_final: 0.6636 (tmm) REVERT: F 280 LEU cc_start: 0.4733 (OUTLIER) cc_final: 0.4514 (tp) REVERT: F 297 MET cc_start: 0.7028 (tpp) cc_final: 0.6759 (tpp) REVERT: F 299 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: F 309 MET cc_start: 0.4986 (mmm) cc_final: 0.4741 (mmm) REVERT: G 162 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6879 (mt-10) REVERT: G 179 ARG cc_start: 0.8004 (ttt-90) cc_final: 0.7567 (ttt-90) outliers start: 40 outliers final: 20 residues processed: 393 average time/residue: 1.6769 time to fit residues: 713.8724 Evaluate side-chains 400 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 373 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 1 optimal weight: 0.0270 chunk 9 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN C 79 ASN D 146 HIS D 286 ASN E 23 GLN F 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088424 restraints weight = 69116.230| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.28 r_work: 0.2965 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4242 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= 0.149 Angle : 0.622 10.037 22607 Z= 0.314 Chirality : 0.040 0.130 2552 Planarity : 0.006 0.098 2808 Dihedral : 14.221 158.776 2588 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.19 % Allowed : 20.11 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1950 helix: 1.06 (0.16), residues: 1062 sheet: 0.45 (0.30), residues: 274 loop : 0.03 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG G 196 TYR 0.017 0.001 TYR C 124 PHE 0.014 0.001 PHE D 197 HIS 0.008 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00343 (16603) covalent geometry : angle 0.62191 (22607) hydrogen bonds : bond 0.04883 ( 812) hydrogen bonds : angle 4.67928 ( 2298) *********************** 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 415 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 379 time to evaluate : 0.832 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9178 (tpp) cc_final: 0.8879 (tpp) REVERT: A 240 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: B 101 LEU cc_start: 0.8935 (mt) cc_final: 0.8720 (mp) REVERT: B 185 ASP cc_start: 0.8297 (m-30) cc_final: 0.8093 (m-30) REVERT: B 252 ASP cc_start: 0.8468 (t0) cc_final: 0.8103 (t0) REVERT: B 291 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7615 (mtp85) REVERT: C 81 LYS cc_start: 0.8403 (mmtm) cc_final: 0.8121 (mmtm) REVERT: C 89 GLU cc_start: 0.7434 (mp0) cc_final: 0.7130 (mm-30) REVERT: C 117 MET cc_start: 0.6670 (tpp) cc_final: 0.6273 (mmm) REVERT: C 182 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7428 (mm-30) REVERT: C 211 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8484 (mtt-85) REVERT: D 89 GLU cc_start: 0.7905 (tp30) cc_final: 0.7699 (tp30) REVERT: D 90 LYS cc_start: 0.8260 (mtmm) cc_final: 0.8040 (ptpt) REVERT: D 105 ASP cc_start: 0.8330 (m-30) cc_final: 0.8008 (m-30) REVERT: D 179 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7188 (pp20) REVERT: D 197 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.5712 (p90) REVERT: D 262 ASP cc_start: 0.8354 (m-30) cc_final: 0.8111 (m-30) REVERT: D 292 GLU cc_start: 0.8380 (pm20) cc_final: 0.8129 (pm20) REVERT: E 68 MET cc_start: 0.8692 (tpp) cc_final: 0.8255 (tpt) REVERT: E 110 ASP cc_start: 0.8094 (t0) cc_final: 0.7724 (t0) REVERT: E 129 ASP cc_start: 0.7636 (t0) cc_final: 0.7246 (t0) REVERT: E 135 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6217 (ttm) REVERT: E 259 ASP cc_start: 0.6993 (t70) cc_final: 0.6767 (t70) REVERT: E 289 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7088 (mm-30) REVERT: E 310 ARG cc_start: 0.7207 (ttm110) cc_final: 0.6976 (mtm180) REVERT: F 105 ASP cc_start: 0.7931 (m-30) cc_final: 0.7657 (m-30) REVERT: F 115 MET cc_start: 0.6553 (tpp) cc_final: 0.6288 (tpp) REVERT: F 199 MET cc_start: 0.7643 (tpp) cc_final: 0.7429 (tpp) REVERT: F 204 GLU cc_start: 0.7508 (tp30) cc_final: 0.7275 (tp30) REVERT: F 269 MET cc_start: 0.7249 (mtp) cc_final: 0.6779 (tmm) REVERT: F 280 LEU cc_start: 0.4696 (OUTLIER) cc_final: 0.4450 (tp) REVERT: F 297 MET cc_start: 0.7044 (tpp) cc_final: 0.6777 (tpp) REVERT: F 299 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: F 309 MET cc_start: 0.5009 (mmm) cc_final: 0.4788 (mmm) REVERT: G 162 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6889 (mt-10) REVERT: G 179 ARG cc_start: 0.8002 (ttt-90) cc_final: 0.7558 (ttt-90) outliers start: 36 outliers final: 18 residues processed: 394 average time/residue: 1.7007 time to fit residues: 726.4967 Evaluate side-chains 402 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 377 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 134 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN D 82 GLN D 146 HIS D 286 ASN E 23 GLN F 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087717 restraints weight = 69321.154| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.27 r_work: 0.2949 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16603 Z= 0.177 Angle : 0.640 10.224 22607 Z= 0.325 Chirality : 0.041 0.150 2552 Planarity : 0.005 0.072 2808 Dihedral : 14.290 159.196 2588 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.07 % Allowed : 20.17 % Favored : 77.76 % 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: 0.79 (0.19), residues: 1950 helix: 1.05 (0.16), residues: 1055 sheet: 0.36 (0.30), residues: 274 loop : -0.12 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 143 TYR 0.018 0.001 TYR C 124 PHE 0.017 0.001 PHE D 197 HIS 0.009 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00414 (16603) covalent geometry : angle 0.63981 (22607) hydrogen bonds : bond 0.05264 ( 812) hydrogen bonds : angle 4.69983 ( 2298) *********************** 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 415 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 381 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9155 (tpp) cc_final: 0.8856 (tpp) REVERT: A 117 MET cc_start: 0.8142 (mmt) cc_final: 0.7862 (mmt) REVERT: A 240 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: B 101 LEU cc_start: 0.8918 (mt) cc_final: 0.8692 (mp) REVERT: B 252 ASP cc_start: 0.8464 (t0) cc_final: 0.8092 (t0) REVERT: B 291 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7612 (mtp85) REVERT: C 81 LYS cc_start: 0.8392 (mmtm) cc_final: 0.8119 (mmtm) REVERT: C 89 GLU cc_start: 0.7453 (mp0) cc_final: 0.7157 (mm-30) REVERT: C 117 MET cc_start: 0.6865 (tpp) cc_final: 0.6445 (mmm) REVERT: C 182 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7409 (mm-30) REVERT: C 211 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8503 (mtt-85) REVERT: D 39 LYS cc_start: 0.8387 (tppt) cc_final: 0.7912 (tppt) REVERT: D 43 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7870 (mm-30) REVERT: D 89 GLU cc_start: 0.8014 (tp30) cc_final: 0.7810 (tp30) REVERT: D 105 ASP cc_start: 0.8344 (m-30) cc_final: 0.8046 (m-30) REVERT: D 120 GLU cc_start: 0.7775 (tt0) cc_final: 0.7391 (tm-30) REVERT: D 179 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: D 197 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.5761 (p90) REVERT: D 262 ASP cc_start: 0.8365 (m-30) cc_final: 0.8126 (m-30) REVERT: D 292 GLU cc_start: 0.8398 (pm20) cc_final: 0.8158 (pm20) REVERT: E 68 MET cc_start: 0.8710 (tpp) cc_final: 0.8266 (tpt) REVERT: E 110 ASP cc_start: 0.8093 (t0) cc_final: 0.7269 (t0) REVERT: E 111 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7617 (mt-10) REVERT: E 129 ASP cc_start: 0.7703 (t0) cc_final: 0.7327 (t0) REVERT: E 135 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5880 (ttm) REVERT: E 259 ASP cc_start: 0.7067 (t70) cc_final: 0.6836 (t70) REVERT: E 289 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7047 (mm-30) REVERT: E 295 GLU cc_start: 0.8308 (tt0) cc_final: 0.7905 (tm-30) REVERT: F 105 ASP cc_start: 0.7969 (m-30) cc_final: 0.7637 (m-30) REVERT: F 115 MET cc_start: 0.6621 (tpp) cc_final: 0.6343 (tpp) REVERT: F 269 MET cc_start: 0.7212 (mtp) cc_final: 0.6766 (tmm) REVERT: F 280 LEU cc_start: 0.4707 (OUTLIER) cc_final: 0.4453 (tp) REVERT: F 289 GLU cc_start: 0.5192 (mm-30) cc_final: 0.4977 (mm-30) REVERT: F 297 MET cc_start: 0.7074 (tpp) cc_final: 0.6817 (tpp) REVERT: F 299 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: F 309 MET cc_start: 0.5012 (mmm) cc_final: 0.4784 (mmm) REVERT: G 162 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6841 (mt-10) REVERT: G 179 ARG cc_start: 0.7956 (ttt-90) cc_final: 0.7551 (ttt-90) outliers start: 34 outliers final: 19 residues processed: 392 average time/residue: 1.6846 time to fit residues: 715.4241 Evaluate side-chains 402 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 376 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 132 optimal weight: 0.0010 chunk 102 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN D 82 GLN D 146 HIS D 286 ASN E 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088457 restraints weight = 69829.097| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.29 r_work: 0.2964 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16603 Z= 0.132 Angle : 0.629 11.320 22607 Z= 0.315 Chirality : 0.040 0.187 2552 Planarity : 0.006 0.117 2808 Dihedral : 14.180 159.573 2588 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.71 % Allowed : 21.21 % Favored : 77.09 % 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: 0.99 (0.19), residues: 1950 helix: 1.19 (0.16), residues: 1061 sheet: 0.40 (0.30), residues: 276 loop : 0.03 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG G 196 TYR 0.017 0.001 TYR C 124 PHE 0.014 0.001 PHE D 197 HIS 0.009 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00305 (16603) covalent geometry : angle 0.62911 (22607) hydrogen bonds : bond 0.04540 ( 812) hydrogen bonds : angle 4.58394 ( 2298) ********************** 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 409 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 381 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9138 (tpp) cc_final: 0.8833 (tpp) REVERT: A 82 GLN cc_start: 0.8174 (tt0) cc_final: 0.7904 (tm-30) REVERT: A 117 MET cc_start: 0.8145 (mmt) cc_final: 0.7877 (mmt) REVERT: A 240 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7582 (m-30) REVERT: B 101 LEU cc_start: 0.8932 (mt) cc_final: 0.8713 (mp) REVERT: B 163 MET cc_start: 0.8797 (ttt) cc_final: 0.8590 (mtp) REVERT: B 252 ASP cc_start: 0.8452 (t0) cc_final: 0.8049 (t0) REVERT: B 291 ARG cc_start: 0.7954 (mtp85) cc_final: 0.7634 (mtp85) REVERT: C 81 LYS cc_start: 0.8389 (mmtm) cc_final: 0.8105 (mmtm) REVERT: C 89 GLU cc_start: 0.7444 (mp0) cc_final: 0.7143 (mm-30) REVERT: C 182 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7415 (mm-30) REVERT: C 211 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8490 (mtt-85) REVERT: D 39 LYS cc_start: 0.8362 (tppt) cc_final: 0.7974 (tppt) REVERT: D 43 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7813 (mm-30) REVERT: D 89 GLU cc_start: 0.8057 (tp30) cc_final: 0.7825 (tp30) REVERT: D 105 ASP cc_start: 0.8324 (m-30) cc_final: 0.8020 (m-30) REVERT: D 179 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7362 (pp20) REVERT: D 197 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.5770 (p90) REVERT: D 242 LYS cc_start: 0.8322 (tppt) cc_final: 0.7902 (tppt) REVERT: D 262 ASP cc_start: 0.8324 (m-30) cc_final: 0.8087 (m-30) REVERT: D 292 GLU cc_start: 0.8384 (pm20) cc_final: 0.8133 (pm20) REVERT: E 68 MET cc_start: 0.8685 (tpp) cc_final: 0.8254 (tpt) REVERT: E 70 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8467 (t80) REVERT: E 110 ASP cc_start: 0.8098 (t0) cc_final: 0.7729 (t0) REVERT: E 129 ASP cc_start: 0.7714 (t0) cc_final: 0.7315 (t0) REVERT: E 135 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.6121 (ttm) REVERT: E 171 ARG cc_start: 0.8329 (mmt90) cc_final: 0.8018 (mpt180) REVERT: E 289 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7060 (mm-30) REVERT: E 310 ARG cc_start: 0.7238 (ttm110) cc_final: 0.6926 (mtm180) REVERT: F 105 ASP cc_start: 0.7908 (m-30) cc_final: 0.7634 (m-30) REVERT: F 115 MET cc_start: 0.6546 (tpp) cc_final: 0.6262 (tpp) REVERT: F 269 MET cc_start: 0.7150 (mtp) cc_final: 0.6798 (tmm) REVERT: F 297 MET cc_start: 0.7041 (tpp) cc_final: 0.6787 (tpp) REVERT: F 309 MET cc_start: 0.5019 (mmm) cc_final: 0.4783 (mmm) REVERT: G 162 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6884 (mt-10) REVERT: G 179 ARG cc_start: 0.7980 (ttt-90) cc_final: 0.7550 (ttt-90) outliers start: 28 outliers final: 14 residues processed: 391 average time/residue: 1.6775 time to fit residues: 712.0161 Evaluate side-chains 398 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 378 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 129 optimal weight: 0.0070 chunk 109 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 71 optimal weight: 0.0970 chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN D 82 GLN D 146 HIS D 286 ASN E 23 GLN F 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.089475 restraints weight = 69477.749| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.31 r_work: 0.2986 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16603 Z= 0.121 Angle : 0.618 10.343 22607 Z= 0.308 Chirality : 0.039 0.191 2552 Planarity : 0.005 0.075 2808 Dihedral : 14.077 160.358 2588 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.46 % Allowed : 21.94 % Favored : 76.60 % 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: 1.18 (0.19), residues: 1950 helix: 1.31 (0.16), residues: 1063 sheet: 0.50 (0.30), residues: 276 loop : 0.16 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 143 TYR 0.016 0.001 TYR C 124 PHE 0.011 0.001 PHE D 197 HIS 0.010 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00279 (16603) covalent geometry : angle 0.61752 (22607) hydrogen bonds : bond 0.04128 ( 812) hydrogen bonds : angle 4.50018 ( 2298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15650.40 seconds wall clock time: 263 minutes 58.75 seconds (15838.75 seconds total)