Starting phenix.real_space_refine on Mon Sep 14 17:38:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbo_13297/09_2026/7pbo_13297_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbo_13297/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pbo_13297/09_2026/7pbo_13297_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbo_13297/09_2026/7pbo_13297_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbo_13297/09_2026/7pbo_13297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbo_13297/09_2026/7pbo_13297.map" } 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-2.2.1-6174/lib/python3.11/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: 5.56, 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: 2.65 Conformation dependent library (CDL) restraints added in 938.7 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: 5.56 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: 7.34 Time building geometry restraints manager: 3.73 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 - 2.27: 58162 2.27 - 4.55: 451 4.55 - 6.82: 50 6.82 - 9.09: 15 9.09 - 11.36: 6 Bond angle restraints: 58684 Sorted by residual: angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 111.80 -3.80 7.00e-01 2.04e+00 2.95e+01 angle pdb=" C4' DT V 15 " pdb=" O4' DT V 15 " pdb=" C1' DT V 15 " ideal model delta sigma weight residual 110.10 105.34 4.76 1.00e+00 1.00e+00 2.27e+01 angle pdb=" O4' DT V 7 " pdb=" C1' DT V 7 " pdb=" N1 DT V 7 " ideal model delta sigma weight residual 108.00 111.06 -3.06 7.00e-01 2.04e+00 1.91e+01 angle pdb=" C4' DC V 8 " pdb=" O4' DC V 8 " pdb=" C1' DC V 8 " ideal model delta sigma weight residual 110.10 105.81 4.29 1.00e+00 1.00e+00 1.84e+01 angle pdb=" N3 DT U 7 " pdb=" C4 DT U 7 " pdb=" O4 DT U 7 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 58679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.46: 14462 31.46 - 62.92: 566 62.92 - 94.38: 34 94.38 - 125.84: 0 125.84 - 157.30: 4 Dihedral angle restraints: 15066 sinusoidal: 8633 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 15063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2262 0.075 - 0.150: 270 0.150 - 0.226: 12 0.226 - 0.301: 3 0.301 - 0.376: 1 Chirality restraints: 2548 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.71 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C3' AGS B 401 " pdb=" C2' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" O3' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 2545 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: 3.030 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: 0.210 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.040 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.005 0.099 16603 Z= 0.259 Angle : 0.788 11.364 22607 Z= 0.459 Chirality : 0.047 0.376 2548 Planarity : 0.010 0.133 2808 Dihedral : 14.838 157.300 6439 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/Z covalent geometry : bond 0.00481 / 0.26 (16603) covalent geometry : angle 0.78822 / 0.46 (22607) hydrogen bonds : bond 0.27203 / 18.05 ( 812) hydrogen bonds : angle 8.52041 / 6.15 ( 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 : 1.054 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: A 312 ARG cc_start: 0.7937 (tpt170) cc_final: 0.7736 (tpt170) 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: 0.7666 (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: 0.7132 (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: 0.8224 (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: 0.8475 (p) REVERT: D 313 THR cc_start: 0.8853 (m) cc_final: 0.8595 (p) REVERT: E 39 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7118 (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: 0.6379 (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: 0.6718 (t70) outliers start: 2 outliers final: 1 residues processed: 516 average time/residue: 1.5999 time to fit residues: 900.7167 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 : 0.884 ------------------------------------------------------------------------------- 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: 2.9990 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... A 82 GLN A 99 ASN C 79 ASN C 166 ASN C 286 ASN D 146 HIS D 166 ASN D 221 ASN D 286 ASN E 23 GLN F 255 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.089238 restraints weight = 69096.471| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.31 r_work: 0.2974 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16603 Z= 0.184 Angle : 0.724 6.835 22607 Z= 0.387 Chirality : 0.044 0.163 2548 Planarity : 0.006 0.054 2808 Dihedral : 13.978 145.710 2629 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.99 % Allowed : 13.95 % Favored : 83.06 % 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: 0.35 (0.18), residues: 1950 helix: 0.20 (0.15), residues: 1063 sheet: 0.71 (0.31), residues: 275 loop : 0.41 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 312 TYR 0.023 0.001 TYR C 124 PHE 0.015 0.001 PHE E 70 HIS 0.007 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (16603) covalent geometry : angle 0.72366 / 0.39 (22607) hydrogen bonds : bond 0.08248 / 5.58 ( 812) hydrogen bonds : angle 5.94590 / 4.25 ( 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 461 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 412 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9268 (tpp) cc_final: 0.8995 (tpp) REVERT: A 144 SER cc_start: 0.8605 (p) cc_final: 0.7946 (t) REVERT: A 240 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: A 292 GLU cc_start: 0.7583 (mp0) cc_final: 0.7379 (mp0) REVERT: A 295 GLU cc_start: 0.7722 (tp30) cc_final: 0.7250 (tp30) REVERT: B 147 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 185 ASP cc_start: 0.8334 (m-30) cc_final: 0.8061 (m-30) REVERT: B 252 ASP cc_start: 0.8495 (t0) cc_final: 0.8081 (t0) REVERT: C 117 MET cc_start: 0.7026 (tpp) cc_final: 0.6138 (tpp) REVERT: C 121 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: C 124 TYR cc_start: 0.8637 (p90) cc_final: 0.8393 (p90) REVERT: D 90 LYS cc_start: 0.8565 (ptmm) cc_final: 0.8271 (ptpt) REVERT: D 197 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.5416 (p90) REVERT: D 242 LYS cc_start: 0.8314 (tppt) cc_final: 0.8059 (tppt) REVERT: D 262 ASP cc_start: 0.8411 (m-30) cc_final: 0.8143 (m-30) REVERT: D 311 THR cc_start: 0.8611 (m) cc_final: 0.8316 (p) REVERT: D 313 THR cc_start: 0.8821 (m) cc_final: 0.8553 (p) REVERT: E 39 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7899 (mtmt) REVERT: E 43 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: E 110 ASP cc_start: 0.8022 (t0) cc_final: 0.7644 (t0) REVERT: E 125 SER cc_start: 0.8448 (m) cc_final: 0.8187 (t) REVERT: E 289 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7143 (mm-30) REVERT: E 291 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7421 (ptm-80) REVERT: F 81 LYS cc_start: 0.8269 (mttt) cc_final: 0.7891 (tptp) REVERT: F 109 ILE cc_start: 0.8900 (mt) cc_final: 0.8674 (mm) REVERT: F 110 ASP cc_start: 0.8077 (t0) cc_final: 0.7822 (t0) REVERT: F 253 VAL cc_start: 0.8802 (t) cc_final: 0.8509 (p) REVERT: F 297 MET cc_start: 0.7205 (tpp) cc_final: 0.6902 (tpp) REVERT: F 299 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6914 (OUTLIER) REVERT: G 179 ARG cc_start: 0.7832 (ttt-90) cc_final: 0.7627 (ttt-90) REVERT: G 180 MET cc_start: 0.7952 (mtp) cc_final: 0.7742 (mtp) REVERT: G 196 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7439 (ttm-80) outliers start: 49 outliers final: 17 residues processed: 434 average time/residue: 1.5452 time to fit residues: 734.4659 Evaluate side-chains 410 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 387 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 E residue 305 LYS 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: 1.9990 chunk 160 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 179 optimal weight: 0.1980 chunk 154 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN B 246 GLN C 79 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.088697 restraints weight = 69436.096| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.30 r_work: 0.2951 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16603 Z= 0.166 Angle : 0.642 7.555 22607 Z= 0.337 Chirality : 0.042 0.189 2548 Planarity : 0.005 0.051 2808 Dihedral : 13.983 146.428 2626 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.68 % Allowed : 16.21 % 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: 0.60 (0.18), residues: 1950 helix: 0.57 (0.16), residues: 1058 sheet: 0.54 (0.30), residues: 284 loop : 0.33 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 143 TYR 0.022 0.001 TYR E 131 PHE 0.012 0.001 PHE D 197 HIS 0.037 0.002 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (16603) covalent geometry : angle 0.64190 / 0.34 (22607) hydrogen bonds : bond 0.07122 / 4.81 ( 812) hydrogen bonds : angle 5.42035 / 3.87 ( 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: 44 poor density : 395 time to evaluate : 0.919 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: A 68 MET cc_start: 0.9260 (tpp) cc_final: 0.8930 (tpp) REVERT: A 144 SER cc_start: 0.8608 (p) cc_final: 0.7984 (t) REVERT: A 240 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: A 295 GLU cc_start: 0.7779 (tp30) cc_final: 0.7386 (tp30) REVERT: B 147 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8129 (mt) REVERT: B 185 ASP cc_start: 0.8280 (m-30) cc_final: 0.8033 (m-30) REVERT: B 252 ASP cc_start: 0.8483 (t0) cc_final: 0.8085 (t0) REVERT: C 46 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8028 (mttt) REVERT: C 53 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7856 (t0) REVERT: C 117 MET cc_start: 0.6644 (tpp) cc_final: 0.5958 (tpp) REVERT: C 121 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: C 124 TYR cc_start: 0.8698 (p90) cc_final: 0.8446 (p90) REVERT: C 199 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8211 (mmm) REVERT: D 90 LYS cc_start: 0.8448 (ptmm) cc_final: 0.8136 (ptpt) REVERT: D 131 TYR cc_start: 0.8666 (p90) cc_final: 0.8379 (p90) REVERT: D 179 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6819 (pp20) REVERT: D 197 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.5482 (p90) REVERT: D 262 ASP cc_start: 0.8405 (m-30) cc_final: 0.8158 (m-30) REVERT: D 313 THR cc_start: 0.8757 (m) cc_final: 0.8515 (p) REVERT: E 43 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: E 68 MET cc_start: 0.8672 (tpp) cc_final: 0.8459 (tpt) REVERT: E 110 ASP cc_start: 0.8088 (t0) cc_final: 0.7714 (t0) REVERT: E 129 ASP cc_start: 0.7554 (t0) cc_final: 0.6794 (t0) REVERT: E 131 TYR cc_start: 0.7781 (p90) cc_final: 0.6968 (p90) REVERT: E 289 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7194 (mm-30) REVERT: F 209 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7947 (tp) REVERT: F 255 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.8012 (t-90) REVERT: F 280 LEU cc_start: 0.4662 (OUTLIER) cc_final: 0.4418 (tp) REVERT: F 297 MET cc_start: 0.7078 (tpp) cc_final: 0.6724 (tpp) REVERT: F 299 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: G 162 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6704 (mt-10) REVERT: G 179 ARG cc_start: 0.7863 (ttt-90) cc_final: 0.7501 (ttt-90) REVERT: G 192 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6828 (pp20) REVERT: G 196 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7140 (ttm110) outliers start: 44 outliers final: 16 residues processed: 411 average time/residue: 1.4877 time to fit residues: 672.2588 Evaluate side-chains 412 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 382 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER 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 145 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 46 LYS 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 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 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 192 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: 0.6980 chunk 45 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN C 79 ASN D 221 ASN E 23 GLN F 177 HIS F 246 GLN ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.089024 restraints weight = 68751.499| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.30 r_work: 0.2960 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16603 Z= 0.154 Angle : 0.626 6.692 22607 Z= 0.325 Chirality : 0.041 0.148 2548 Planarity : 0.005 0.058 2808 Dihedral : 13.977 149.051 2624 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.44 % Allowed : 17.67 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 1950 helix: 0.75 (0.16), residues: 1059 sheet: 0.56 (0.30), residues: 276 loop : 0.22 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 312 TYR 0.019 0.001 TYR C 124 PHE 0.012 0.001 PHE D 197 HIS 0.038 0.002 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (16603) covalent geometry : angle 0.62599 / 0.32 (22607) hydrogen bonds : bond 0.06056 / 4.10 ( 812) hydrogen bonds : angle 5.17847 / 3.68 ( 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 429 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 389 time to evaluate : 0.893 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: 0.9227 (tpp) cc_final: 0.8891 (tpp) REVERT: A 82 GLN cc_start: 0.8186 (tt0) cc_final: 0.7920 (tm-30) REVERT: A 144 SER cc_start: 0.8616 (p) cc_final: 0.7991 (t) REVERT: A 295 GLU cc_start: 0.7816 (tp30) cc_final: 0.7550 (tp30) REVERT: B 147 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8081 (mt) REVERT: B 185 ASP cc_start: 0.8305 (m-30) cc_final: 0.8075 (m-30) REVERT: B 252 ASP cc_start: 0.8474 (t0) cc_final: 0.8063 (t0) REVERT: B 291 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7772 (mtp85) REVERT: C 46 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8049 (mttt) REVERT: C 117 MET cc_start: 0.6652 (tpp) cc_final: 0.5721 (tpp) REVERT: C 121 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: C 124 TYR cc_start: 0.8712 (p90) cc_final: 0.8512 (p90) REVERT: C 199 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8227 (mmm) REVERT: C 211 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8432 (mtt-85) REVERT: D 90 LYS cc_start: 0.8370 (ptmm) cc_final: 0.8109 (ptpt) REVERT: D 120 GLU cc_start: 0.7673 (tt0) cc_final: 0.7051 (tt0) REVERT: D 179 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6901 (pp20) REVERT: D 197 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.5519 (p90) REVERT: D 262 ASP cc_start: 0.8367 (m-30) cc_final: 0.8103 (m-30) REVERT: D 311 THR cc_start: 0.8505 (m) cc_final: 0.8219 (p) REVERT: D 313 THR cc_start: 0.8740 (m) cc_final: 0.8535 (p) REVERT: E 110 ASP cc_start: 0.8087 (t0) cc_final: 0.7716 (t0) REVERT: E 129 ASP cc_start: 0.7554 (t0) cc_final: 0.6805 (t0) REVERT: E 131 TYR cc_start: 0.7696 (p90) cc_final: 0.6949 (p90) REVERT: E 289 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7128 (mm-30) REVERT: F 43 GLU cc_start: 0.7489 (tp30) cc_final: 0.7254 (tp30) REVERT: F 204 GLU cc_start: 0.7440 (tp30) cc_final: 0.7205 (tp30) REVERT: F 209 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7886 (tp) REVERT: F 280 LEU cc_start: 0.4666 (OUTLIER) cc_final: 0.4423 (tp) REVERT: F 297 MET cc_start: 0.6967 (tpp) cc_final: 0.6588 (tpp) REVERT: F 299 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: G 162 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6774 (mt-10) REVERT: G 192 GLU cc_start: 0.7201 (pp20) cc_final: 0.6892 (pp20) REVERT: G 196 ARG cc_start: 0.7493 (ttm110) cc_final: 0.7243 (ttm110) outliers start: 40 outliers final: 14 residues processed: 403 average time/residue: 1.5964 time to fit residues: 704.8068 Evaluate side-chains 408 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 384 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 46 LYS Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 199 MET 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 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 188 GLU 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: 5.9990 chunk 178 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 HIS C 79 ASN D 146 HIS D 286 ASN E 23 GLN F 246 GLN ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.118577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.088083 restraints weight = 69308.759| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.30 r_work: 0.2948 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3786 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= 0.186 Angle : 0.632 6.792 22607 Z= 0.328 Chirality : 0.042 0.154 2548 Planarity : 0.005 0.050 2808 Dihedral : 14.049 154.970 2624 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.50 % Allowed : 18.46 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1950 helix: 0.80 (0.16), residues: 1057 sheet: 0.54 (0.30), residues: 277 loop : 0.06 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 312 TYR 0.019 0.001 TYR C 124 PHE 0.015 0.001 PHE D 197 HIS 0.007 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (16603) covalent geometry : angle 0.63183 / 0.33 (22607) hydrogen bonds : bond 0.06080 / 4.11 ( 812) hydrogen bonds : angle 5.07247 / 3.61 ( 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 427 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 386 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9221 (tpp) cc_final: 0.8899 (tpp) REVERT: A 144 SER cc_start: 0.8594 (p) cc_final: 0.7957 (t) REVERT: A 240 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: A 295 GLU cc_start: 0.7789 (tp30) cc_final: 0.7525 (tp30) REVERT: B 185 ASP cc_start: 0.8327 (m-30) cc_final: 0.8111 (m-30) REVERT: B 252 ASP cc_start: 0.8478 (t0) cc_final: 0.8071 (t0) REVERT: B 291 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7738 (mtp85) REVERT: C 46 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8037 (mttt) REVERT: C 117 MET cc_start: 0.6560 (tpp) cc_final: 0.5771 (tpp) REVERT: C 121 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: C 182 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7537 (mm-30) REVERT: C 199 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8225 (mmm) REVERT: C 211 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8470 (mtt-85) REVERT: D 90 LYS cc_start: 0.8322 (ptmm) cc_final: 0.8091 (ptpt) REVERT: D 105 ASP cc_start: 0.8391 (m-30) cc_final: 0.8090 (m-30) REVERT: D 114 ARG cc_start: 0.8089 (ttm110) cc_final: 0.7823 (mtp180) REVERT: D 120 GLU cc_start: 0.7658 (tt0) cc_final: 0.7160 (tt0) REVERT: D 179 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6990 (pp20) REVERT: D 197 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.5669 (p90) REVERT: D 262 ASP cc_start: 0.8400 (m-30) cc_final: 0.8144 (m-30) REVERT: D 292 GLU cc_start: 0.8290 (pm20) cc_final: 0.8060 (pm20) REVERT: E 68 MET cc_start: 0.8685 (tpp) cc_final: 0.8211 (tpt) REVERT: E 110 ASP cc_start: 0.8092 (t0) cc_final: 0.7728 (t0) REVERT: E 129 ASP cc_start: 0.7627 (t0) cc_final: 0.6940 (t0) REVERT: E 289 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7134 (mm-30) REVERT: E 295 GLU cc_start: 0.8417 (tt0) cc_final: 0.7927 (tm-30) REVERT: F 43 GLU cc_start: 0.7579 (tp30) cc_final: 0.7301 (tp30) REVERT: F 209 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7842 (tp) REVERT: F 280 LEU cc_start: 0.4751 (OUTLIER) cc_final: 0.4539 (tp) REVERT: F 297 MET cc_start: 0.7038 (tpp) cc_final: 0.6697 (tpp) REVERT: F 299 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: G 162 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6781 (mt-10) REVERT: G 192 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6980 (pp20) REVERT: G 196 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7253 (ttm110) outliers start: 41 outliers final: 19 residues processed: 402 average time/residue: 1.5726 time to fit residues: 692.8065 Evaluate side-chains 408 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 378 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 128 GLU 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 46 LYS Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 199 MET 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 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 295 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 188 GLU 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 192 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: 0.0470 chunk 120 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 ASN D 146 HIS D 221 ASN D 286 ASN E 23 GLN E 99 ASN F 246 GLN ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.088898 restraints weight = 69102.768| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.29 r_work: 0.2967 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3946 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= 0.144 Angle : 0.618 8.096 22607 Z= 0.318 Chirality : 0.041 0.159 2548 Planarity : 0.005 0.054 2808 Dihedral : 13.966 156.224 2624 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.68 % Allowed : 18.28 % Favored : 79.04 % 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: 0.93 (0.16), residues: 1058 sheet: 0.54 (0.30), residues: 277 loop : 0.06 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 143 TYR 0.020 0.001 TYR D 131 PHE 0.013 0.001 PHE D 197 HIS 0.007 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16603) covalent geometry : angle 0.61769 / 0.32 (22607) hydrogen bonds : bond 0.05410 / 3.64 ( 812) hydrogen bonds : angle 4.92903 / 3.50 ( 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 425 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 381 time to evaluate : 0.900 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: 0.9186 (tpp) cc_final: 0.8862 (tpp) REVERT: A 144 SER cc_start: 0.8609 (p) cc_final: 0.7939 (t) REVERT: A 240 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: A 295 GLU cc_start: 0.7796 (tp30) cc_final: 0.7561 (tp30) REVERT: B 185 ASP cc_start: 0.8284 (m-30) cc_final: 0.8077 (m-30) REVERT: B 252 ASP cc_start: 0.8474 (t0) cc_final: 0.8112 (t0) REVERT: B 291 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7665 (mtp85) REVERT: C 46 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8003 (mttt) REVERT: C 117 MET cc_start: 0.6487 (tpp) cc_final: 0.5658 (tpp) REVERT: C 121 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: C 182 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7470 (mm-30) REVERT: C 211 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8499 (mtt-85) REVERT: D 89 GLU cc_start: 0.7897 (tp30) cc_final: 0.7667 (tp30) REVERT: D 90 LYS cc_start: 0.8308 (ptmm) cc_final: 0.8095 (ptpt) REVERT: D 105 ASP cc_start: 0.8369 (m-30) cc_final: 0.8051 (m-30) REVERT: D 120 GLU cc_start: 0.7608 (tt0) cc_final: 0.7136 (tt0) REVERT: D 179 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7127 (pp20) REVERT: D 197 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.5663 (p90) REVERT: D 262 ASP cc_start: 0.8349 (m-30) cc_final: 0.8091 (m-30) REVERT: D 292 GLU cc_start: 0.8288 (pm20) cc_final: 0.8052 (pm20) REVERT: D 311 THR cc_start: 0.8427 (m) cc_final: 0.8149 (p) REVERT: E 68 MET cc_start: 0.8673 (tpp) cc_final: 0.8183 (tpt) REVERT: E 110 ASP cc_start: 0.8090 (t0) cc_final: 0.7721 (t0) REVERT: E 129 ASP cc_start: 0.7515 (t0) cc_final: 0.7006 (t0) REVERT: E 192 ARG cc_start: 0.8182 (tpp-160) cc_final: 0.7826 (tpp-160) REVERT: E 289 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7113 (mm-30) REVERT: E 295 GLU cc_start: 0.8385 (tt0) cc_final: 0.7907 (tm-30) REVERT: F 43 GLU cc_start: 0.7614 (tp30) cc_final: 0.7303 (tp30) REVERT: F 110 ASP cc_start: 0.8041 (t0) cc_final: 0.7515 (t0) REVERT: F 111 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7405 (mp0) REVERT: F 199 MET cc_start: 0.7542 (tpp) cc_final: 0.7322 (tpp) REVERT: F 204 GLU cc_start: 0.7502 (tp30) cc_final: 0.7254 (tp30) REVERT: F 209 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7820 (tp) REVERT: F 269 MET cc_start: 0.7109 (mtp) cc_final: 0.6668 (tmm) REVERT: F 280 LEU cc_start: 0.4756 (OUTLIER) cc_final: 0.4542 (tp) REVERT: F 297 MET cc_start: 0.6982 (tpp) cc_final: 0.6699 (tpp) REVERT: F 299 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: G 162 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6852 (mt-10) REVERT: G 179 ARG cc_start: 0.8025 (ttt-90) cc_final: 0.7615 (ttt-90) outliers start: 44 outliers final: 18 residues processed: 399 average time/residue: 1.5967 time to fit residues: 697.8892 Evaluate side-chains 404 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 377 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 46 LYS 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 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 188 GLU 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: 1.9990 chunk 113 optimal weight: 0.9990 chunk 141 optimal weight: 0.5980 chunk 166 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 ASN D 146 HIS D 286 ASN E 23 GLN F 246 GLN ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.088515 restraints weight = 69376.288| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.29 r_work: 0.2956 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16603 Z= 0.160 Angle : 0.621 9.024 22607 Z= 0.318 Chirality : 0.041 0.159 2548 Planarity : 0.005 0.067 2808 Dihedral : 13.934 157.730 2624 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.19 % Allowed : 19.26 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1950 helix: 0.97 (0.16), residues: 1058 sheet: 0.49 (0.30), residues: 276 loop : -0.01 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 196 TYR 0.017 0.001 TYR C 124 PHE 0.015 0.001 PHE D 197 HIS 0.008 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (16603) covalent geometry : angle 0.62062 / 0.32 (22607) hydrogen bonds : bond 0.05395 / 3.64 ( 812) hydrogen bonds : angle 4.87829 / 3.47 ( 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: 36 poor density : 380 time to evaluate : 0.874 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: A 68 MET cc_start: 0.9186 (tpp) cc_final: 0.8870 (tpp) REVERT: A 144 SER cc_start: 0.8598 (p) cc_final: 0.7931 (t) REVERT: A 240 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: A 295 GLU cc_start: 0.7792 (tp30) cc_final: 0.7550 (tp30) REVERT: B 185 ASP cc_start: 0.8294 (m-30) cc_final: 0.8091 (m-30) REVERT: B 252 ASP cc_start: 0.8481 (t0) cc_final: 0.8098 (t0) REVERT: B 291 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7649 (mtp85) REVERT: C 46 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8027 (mttt) REVERT: C 117 MET cc_start: 0.6471 (tpp) cc_final: 0.5565 (tpp) REVERT: C 121 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: C 182 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7444 (mm-30) REVERT: C 211 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8503 (mtt-85) REVERT: D 105 ASP cc_start: 0.8376 (m-30) cc_final: 0.8068 (m-30) REVERT: D 120 GLU cc_start: 0.7617 (tt0) cc_final: 0.7191 (tt0) REVERT: D 129 ASP cc_start: 0.7817 (t70) cc_final: 0.7538 (t0) REVERT: D 179 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7173 (pp20) REVERT: D 197 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.5676 (p90) REVERT: D 262 ASP cc_start: 0.8378 (m-30) cc_final: 0.8132 (m-30) REVERT: D 292 GLU cc_start: 0.8306 (pm20) cc_final: 0.8074 (pm20) REVERT: D 311 THR cc_start: 0.8389 (m) cc_final: 0.8104 (p) REVERT: E 68 MET cc_start: 0.8692 (tpp) cc_final: 0.8206 (tpt) REVERT: E 110 ASP cc_start: 0.8099 (t0) cc_final: 0.7324 (t0) REVERT: E 111 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7610 (mt-10) REVERT: E 129 ASP cc_start: 0.7487 (t0) cc_final: 0.7081 (t0) REVERT: E 289 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7073 (mm-30) REVERT: E 295 GLU cc_start: 0.8384 (tt0) cc_final: 0.7976 (tm-30) REVERT: F 43 GLU cc_start: 0.7622 (tp30) cc_final: 0.7283 (tp30) REVERT: F 105 ASP cc_start: 0.7979 (m-30) cc_final: 0.7667 (m-30) REVERT: F 110 ASP cc_start: 0.8060 (t0) cc_final: 0.7542 (t0) REVERT: F 111 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7245 (mp0) REVERT: F 269 MET cc_start: 0.7056 (mtp) cc_final: 0.6578 (tmm) REVERT: F 280 LEU cc_start: 0.4771 (OUTLIER) cc_final: 0.4549 (tp) REVERT: F 297 MET cc_start: 0.7038 (tpp) cc_final: 0.6736 (tpp) REVERT: F 299 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: G 162 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6848 (mt-10) REVERT: G 179 ARG cc_start: 0.8032 (ttt-90) cc_final: 0.7594 (ttt-90) outliers start: 36 outliers final: 16 residues processed: 396 average time/residue: 1.5604 time to fit residues: 678.2707 Evaluate side-chains 399 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 375 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 93 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain D residue 46 LYS 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 39 LYS 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 188 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 162 optimal weight: 0.3980 chunk 188 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 ASN D 146 HIS D 286 ASN E 23 GLN ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.089609 restraints weight = 69285.153| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.30 r_work: 0.2984 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16603 Z= 0.127 Angle : 0.624 10.447 22607 Z= 0.315 Chirality : 0.040 0.158 2548 Planarity : 0.005 0.093 2808 Dihedral : 13.811 157.001 2624 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.01 % Allowed : 19.80 % Favored : 78.18 % 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: 0.96 (0.19), residues: 1950 helix: 1.10 (0.16), residues: 1062 sheet: 0.54 (0.30), residues: 276 loop : 0.07 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 143 TYR 0.015 0.001 TYR C 124 PHE 0.013 0.001 PHE D 197 HIS 0.008 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16603) covalent geometry : angle 0.62359 / 0.31 (22607) hydrogen bonds : bond 0.04693 / 3.15 ( 812) hydrogen bonds : angle 4.72435 / 3.36 ( 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 416 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 383 time to evaluate : 0.917 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: 0.9175 (tpp) cc_final: 0.8856 (tpp) REVERT: A 82 GLN cc_start: 0.8186 (tt0) cc_final: 0.7916 (tm-30) REVERT: A 144 SER cc_start: 0.8581 (p) cc_final: 0.7928 (t) REVERT: A 240 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7431 (m-30) REVERT: A 295 GLU cc_start: 0.7770 (tp30) cc_final: 0.7539 (tp30) REVERT: B 101 LEU cc_start: 0.8930 (mt) cc_final: 0.8723 (mp) REVERT: B 185 ASP cc_start: 0.8277 (m-30) cc_final: 0.8062 (m-30) REVERT: B 252 ASP cc_start: 0.8462 (t0) cc_final: 0.8076 (t0) REVERT: B 291 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7631 (mtp85) REVERT: C 46 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7986 (mttt) REVERT: C 117 MET cc_start: 0.6417 (tpp) cc_final: 0.5826 (mmm) REVERT: C 182 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7390 (mm-30) REVERT: C 211 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8484 (mtt-85) REVERT: D 89 GLU cc_start: 0.7943 (tp30) cc_final: 0.7714 (tp30) REVERT: D 105 ASP cc_start: 0.8370 (m-30) cc_final: 0.8057 (m-30) REVERT: D 114 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7762 (mtp180) REVERT: D 179 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7114 (pp20) REVERT: D 197 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.5644 (p90) REVERT: D 262 ASP cc_start: 0.8324 (m-30) cc_final: 0.8078 (m-30) REVERT: D 292 GLU cc_start: 0.8326 (pm20) cc_final: 0.8074 (pm20) REVERT: D 311 THR cc_start: 0.8341 (m) cc_final: 0.8062 (p) REVERT: E 68 MET cc_start: 0.8659 (tpp) cc_final: 0.8212 (tpt) REVERT: E 110 ASP cc_start: 0.8104 (t0) cc_final: 0.7734 (t0) REVERT: E 129 ASP cc_start: 0.7524 (t0) cc_final: 0.7079 (t0) REVERT: E 289 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7103 (mm-30) REVERT: E 295 GLU cc_start: 0.8332 (tt0) cc_final: 0.7910 (tm-30) REVERT: E 310 ARG cc_start: 0.7144 (ttm110) cc_final: 0.6933 (mtm180) REVERT: F 43 GLU cc_start: 0.7619 (tp30) cc_final: 0.7393 (tp30) REVERT: F 105 ASP cc_start: 0.7913 (m-30) cc_final: 0.7579 (m-30) REVERT: F 110 ASP cc_start: 0.8113 (t0) cc_final: 0.7567 (t0) REVERT: F 111 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7210 (mp0) REVERT: F 204 GLU cc_start: 0.7471 (tp30) cc_final: 0.7236 (tp30) REVERT: F 269 MET cc_start: 0.7141 (mtp) cc_final: 0.6667 (tmm) REVERT: F 280 LEU cc_start: 0.4744 (OUTLIER) cc_final: 0.4525 (tp) REVERT: F 297 MET cc_start: 0.7017 (tpp) cc_final: 0.6739 (tpp) REVERT: F 299 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: G 162 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6978 (mt-10) REVERT: G 179 ARG cc_start: 0.8013 (ttt-90) cc_final: 0.7587 (ttt-90) outliers start: 33 outliers final: 14 residues processed: 396 average time/residue: 1.5217 time to fit residues: 660.6481 Evaluate side-chains 394 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 373 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 46 LYS Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 160 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 F residue 83 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 134 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 135 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 ASN D 82 GLN D 146 HIS D 286 ASN E 23 GLN F 246 GLN ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.088588 restraints weight = 69198.448| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.28 r_work: 0.2971 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4187 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= 0.161 Angle : 0.626 8.581 22607 Z= 0.319 Chirality : 0.040 0.155 2548 Planarity : 0.006 0.080 2808 Dihedral : 13.830 158.290 2624 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.71 % Allowed : 20.35 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 1950 helix: 1.09 (0.16), residues: 1062 sheet: 0.47 (0.30), residues: 276 loop : 0.00 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 143 TYR 0.018 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/Z covalent geometry : bond 0.00368 / 0.16 (16603) covalent geometry : angle 0.62627 / 0.32 (22607) hydrogen bonds : bond 0.05086 / 3.42 ( 812) hydrogen bonds : angle 4.73925 / 3.37 ( 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 401 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 373 time to evaluate : 0.841 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: 0.9197 (tpp) cc_final: 0.8890 (tpp) REVERT: A 135 MET cc_start: 0.8495 (mmm) cc_final: 0.8272 (mmm) REVERT: A 144 SER cc_start: 0.8569 (p) cc_final: 0.7924 (t) REVERT: A 240 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: B 101 LEU cc_start: 0.8912 (mt) cc_final: 0.8693 (mp) REVERT: B 185 ASP cc_start: 0.8278 (m-30) cc_final: 0.8071 (m-30) REVERT: B 252 ASP cc_start: 0.8460 (t0) cc_final: 0.8088 (t0) REVERT: B 291 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7640 (mtp85) REVERT: C 81 LYS cc_start: 0.8386 (mmtm) cc_final: 0.8095 (mmtm) REVERT: C 117 MET cc_start: 0.6763 (tpp) cc_final: 0.5910 (tpp) REVERT: C 121 GLU cc_start: 0.7602 (mp0) cc_final: 0.7009 (mp0) REVERT: C 182 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7383 (mm-30) REVERT: C 211 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8495 (mtt-85) REVERT: D 90 LYS cc_start: 0.8355 (mtmm) cc_final: 0.8126 (ptpt) REVERT: D 105 ASP cc_start: 0.8368 (m-30) cc_final: 0.8073 (m-30) REVERT: D 120 GLU cc_start: 0.7747 (tt0) cc_final: 0.7237 (tm-30) REVERT: D 179 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7119 (pp20) REVERT: D 197 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.5677 (p90) REVERT: D 262 ASP cc_start: 0.8370 (m-30) cc_final: 0.8121 (m-30) REVERT: D 292 GLU cc_start: 0.8335 (pm20) cc_final: 0.8087 (pm20) REVERT: D 311 THR cc_start: 0.8390 (m) cc_final: 0.8186 (p) REVERT: E 68 MET cc_start: 0.8695 (tpp) cc_final: 0.8220 (tpt) REVERT: E 110 ASP cc_start: 0.8086 (t0) cc_final: 0.7272 (t0) REVERT: E 111 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7600 (mt-10) REVERT: E 129 ASP cc_start: 0.7556 (t0) cc_final: 0.7066 (t0) REVERT: E 289 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7105 (mm-30) REVERT: E 295 GLU cc_start: 0.8331 (tt0) cc_final: 0.7906 (tm-30) REVERT: F 43 GLU cc_start: 0.7655 (tp30) cc_final: 0.7384 (tp30) REVERT: F 105 ASP cc_start: 0.7944 (m-30) cc_final: 0.7630 (m-30) REVERT: F 204 GLU cc_start: 0.7508 (tp30) cc_final: 0.7280 (tp30) REVERT: F 269 MET cc_start: 0.7122 (mtp) cc_final: 0.6664 (tmm) REVERT: F 280 LEU cc_start: 0.4698 (OUTLIER) cc_final: 0.4465 (tp) REVERT: F 297 MET cc_start: 0.7021 (tpp) cc_final: 0.6747 (tpp) REVERT: F 299 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: G 162 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6897 (mt-10) REVERT: G 179 ARG cc_start: 0.8014 (ttt-90) cc_final: 0.7579 (ttt-90) outliers start: 28 outliers final: 16 residues processed: 384 average time/residue: 1.4893 time to fit residues: 626.0094 Evaluate side-chains 388 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 366 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 149 LEU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 133 ASP 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 F residue 84 SER 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 192 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: 0.4980 chunk 139 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3556 r_free = 0.3556 target = 0.119461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.089127 restraints weight = 69593.881| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.29 r_work: 0.2969 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16603 Z= 0.140 Angle : 0.634 11.161 22607 Z= 0.321 Chirality : 0.040 0.150 2548 Planarity : 0.006 0.084 2808 Dihedral : 13.781 157.989 2624 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.46 % Allowed : 21.02 % Favored : 77.51 % 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: 0.98 (0.19), residues: 1950 helix: 1.16 (0.16), residues: 1061 sheet: 0.43 (0.30), residues: 274 loop : 0.06 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 196 TYR 0.017 0.001 TYR C 124 PHE 0.013 0.001 PHE D 197 HIS 0.009 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16603) covalent geometry : angle 0.63375 / 0.32 (22607) hydrogen bonds : bond 0.04810 / 3.22 ( 812) hydrogen bonds : angle 4.68828 / 3.33 ( 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 400 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 376 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9181 (tpp) cc_final: 0.8873 (tpp) REVERT: A 82 GLN cc_start: 0.8200 (tt0) cc_final: 0.7912 (tm-30) REVERT: A 117 MET cc_start: 0.8098 (mmt) cc_final: 0.7796 (mmt) REVERT: A 240 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: B 101 LEU cc_start: 0.8934 (mt) cc_final: 0.8724 (mp) REVERT: B 185 ASP cc_start: 0.8286 (m-30) cc_final: 0.8079 (m-30) REVERT: B 252 ASP cc_start: 0.8442 (t0) cc_final: 0.8082 (t0) REVERT: B 291 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7631 (mtp85) REVERT: C 81 LYS cc_start: 0.8388 (mmtm) cc_final: 0.8095 (mmtm) REVERT: C 117 MET cc_start: 0.6565 (tpp) cc_final: 0.6222 (mmm) REVERT: C 182 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7386 (mm-30) REVERT: C 211 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8486 (mtt-85) REVERT: D 105 ASP cc_start: 0.8357 (m-30) cc_final: 0.8057 (m-30) REVERT: D 120 GLU cc_start: 0.7683 (tt0) cc_final: 0.7256 (tm-30) REVERT: D 179 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7141 (pp20) REVERT: D 197 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.5668 (p90) REVERT: D 262 ASP cc_start: 0.8354 (m-30) cc_final: 0.8115 (m-30) REVERT: D 292 GLU cc_start: 0.8356 (pm20) cc_final: 0.8112 (pm20) REVERT: E 68 MET cc_start: 0.8682 (tpp) cc_final: 0.8215 (tpt) REVERT: E 110 ASP cc_start: 0.8084 (t0) cc_final: 0.7719 (t0) REVERT: E 129 ASP cc_start: 0.7606 (t0) cc_final: 0.7210 (t0) REVERT: E 259 ASP cc_start: 0.6954 (t70) cc_final: 0.6685 (t70) REVERT: E 289 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7103 (mm-30) REVERT: E 295 GLU cc_start: 0.8318 (tt0) cc_final: 0.7906 (tm-30) REVERT: E 310 ARG cc_start: 0.7152 (ttm110) cc_final: 0.6869 (mtm180) REVERT: F 43 GLU cc_start: 0.7669 (tp30) cc_final: 0.7387 (tp30) REVERT: F 105 ASP cc_start: 0.7939 (m-30) cc_final: 0.7656 (m-30) REVERT: F 204 GLU cc_start: 0.7527 (tp30) cc_final: 0.7284 (tp30) REVERT: F 269 MET cc_start: 0.7187 (mtp) cc_final: 0.6751 (tmm) REVERT: F 280 LEU cc_start: 0.4715 (OUTLIER) cc_final: 0.4483 (tp) REVERT: F 297 MET cc_start: 0.7034 (tpp) cc_final: 0.6760 (tpp) REVERT: F 299 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: G 179 ARG cc_start: 0.8011 (ttt-90) cc_final: 0.7557 (ttt-90) outliers start: 24 outliers final: 13 residues processed: 385 average time/residue: 1.5280 time to fit residues: 645.7972 Evaluate side-chains 389 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 370 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 46 LYS 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 F residue 84 SER 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 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 101 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3551 r_free = 0.3551 target = 0.119122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088709 restraints weight = 69515.918| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.30 r_work: 0.2967 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16603 Z= 0.149 Angle : 0.634 10.512 22607 Z= 0.323 Chirality : 0.040 0.149 2548 Planarity : 0.006 0.103 2808 Dihedral : 13.776 158.446 2624 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.77 % Allowed : 21.27 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 1950 helix: 1.16 (0.16), residues: 1061 sheet: 0.41 (0.30), residues: 274 loop : 0.03 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 196 TYR 0.018 0.001 TYR C 124 PHE 0.014 0.001 PHE D 197 HIS 0.010 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16603) covalent geometry : angle 0.63386 / 0.32 (22607) hydrogen bonds : bond 0.04897 / 3.30 ( 812) hydrogen bonds : angle 4.67813 / 3.32 ( 2298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15325.69 seconds wall clock time: 258 minutes 48.93 seconds (15528.93 seconds total)