Starting phenix.real_space_refine on Sun Sep 13 15:23:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sqy_55122/09_2026/9sqy_55122.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sqy_55122/09_2026/9sqy_55122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sqy_55122/09_2026/9sqy_55122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sqy_55122/09_2026/9sqy_55122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sqy_55122/09_2026/9sqy_55122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sqy_55122/09_2026/9sqy_55122.map" } resolution = 2.92 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 128 5.16 5 C 15046 2.51 5 N 4032 2.21 5 O 4451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s 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: 23659 Number of models: 1 Model: "" Number of chains: 18 Chain: "D" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2639 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 6, 'TRANS': 322} Chain: "E" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3061 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 28, 'TRANS': 352} Chain: "F" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3052 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 28, 'TRANS': 351} Chain: "G" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1880 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 16, 'TRANS': 219} Chain: "H" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1896 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain: "I" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 7, 'TRANS': 50} Chain: "J" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 7, 'TRANS': 50} Chain: "K" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "L" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "M" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 589 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "O" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "P" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2494 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2099 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 2089 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 260, 2089 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain breaks: 2 bond proxies already assigned to first conformer: 2113 Chain: "B" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2007 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ARG K 74 " occ=0.03 ... (9 atoms not shown) pdb=" NH2 ARG K 74 " occ=0.03 residue: pdb=" N GLY K 75 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY K 75 " occ=0.00 residue: pdb=" N GLY K 76 " occ=0.28 ... (3 atoms not shown) pdb=" OXT GLY K 76 " occ=0.28 residue: pdb=" N LEU N 73 " occ=0.36 ... (6 atoms not shown) pdb=" CD2 LEU N 73 " occ=0.36 residue: pdb=" N ARG N 74 " occ=0.27 ... (9 atoms not shown) pdb=" NH2 ARG N 74 " occ=0.27 residue: pdb=" N GLY N 75 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 75 " occ=0.00 residue: pdb=" N ARG O 74 " occ=0.49 ... (9 atoms not shown) pdb=" NH2 ARG O 74 " occ=0.00 residue: pdb=" N AHIS A 73 " occ=0.70 ... (18 atoms not shown) pdb=" NE2BHIS A 73 " occ=0.30 Time building chain proxies: 5.30, per 1000 atoms: 0.22 Number of scatterers: 23659 At special positions: 0 Unit cell: (108.04, 147.26, 236.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 128 16.00 O 4451 8.00 N 4032 7.00 C 15046 6.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 124 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 122 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 124 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 122 " 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5608 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 24 sheets defined 37.5% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.994A pdb=" N ALA D 17 " --> pdb=" O PHE D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.509A pdb=" N LYS D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 174 removed outlier: 3.615A pdb=" N MET D 173 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 198 removed outlier: 3.727A pdb=" N HIS D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.520A pdb=" N PHE D 202 " --> pdb=" O HIS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 256 removed outlier: 3.729A pdb=" N HIS D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 287 removed outlier: 3.831A pdb=" N PHE D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 295 removed outlier: 3.627A pdb=" N GLU D 292 " --> pdb=" O PRO D 289 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N PHE D 293 " --> pdb=" O ASN D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 14 through 25 removed outlier: 3.665A pdb=" N VAL E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 98 Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 111 through 132 removed outlier: 3.527A pdb=" N LEU E 132 " --> pdb=" O GLN E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 148 removed outlier: 3.731A pdb=" N TYR E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 removed outlier: 4.682A pdb=" N GLU E 153 " --> pdb=" O PRO E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 229 removed outlier: 3.528A pdb=" N HIS E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 282 Processing helix chain 'E' and resid 317 through 321 Processing helix chain 'E' and resid 354 through 370 removed outlier: 3.569A pdb=" N ALA E 362 " --> pdb=" O MET E 358 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 368 " --> pdb=" O ALA E 364 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL E 370 " --> pdb=" O PHE E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 380 removed outlier: 3.710A pdb=" N GLN E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 8 removed outlier: 3.578A pdb=" N LEU F 7 " --> pdb=" O PRO F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 25 removed outlier: 3.632A pdb=" N VAL F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 111 through 132 Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 138 through 147 removed outlier: 3.545A pdb=" N GLU F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 164 through 168 removed outlier: 3.528A pdb=" N GLY F 167 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU F 168 " --> pdb=" O TRP F 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 164 through 168' Processing helix chain 'F' and resid 222 through 229 removed outlier: 3.705A pdb=" N HIS F 227 " --> pdb=" O PRO F 223 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 282 removed outlier: 3.831A pdb=" N TYR F 249 " --> pdb=" O CYS F 245 " (cutoff:3.500A) Proline residue: F 251 - end of helix removed outlier: 4.072A pdb=" N GLN F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR F 263 " --> pdb=" O ASN F 259 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL F 264 " --> pdb=" O LYS F 260 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY F 267 " --> pdb=" O TYR F 263 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE F 278 " --> pdb=" O TYR F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 367 removed outlier: 3.678A pdb=" N LYS F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 380 removed outlier: 4.284A pdb=" N GLU F 375 " --> pdb=" O PRO F 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 106 removed outlier: 4.024A pdb=" N MET G 105 " --> pdb=" O SER G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 139 removed outlier: 4.187A pdb=" N MET G 127 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU G 129 " --> pdb=" O GLN G 125 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE G 138 " --> pdb=" O THR G 134 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 172 removed outlier: 4.115A pdb=" N SER G 168 " --> pdb=" O ARG G 164 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 192 removed outlier: 3.583A pdb=" N PHE G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 235 removed outlier: 4.407A pdb=" N LYS G 233 " --> pdb=" O THR G 229 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET G 235 " --> pdb=" O PRO G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 268 removed outlier: 3.712A pdb=" N PHE G 265 " --> pdb=" O TRP G 261 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA G 266 " --> pdb=" O LYS G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 298 removed outlier: 3.772A pdb=" N MET G 295 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA G 296 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS G 297 " --> pdb=" O ASN G 293 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU G 298 " --> pdb=" O CYS G 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 107 removed outlier: 4.245A pdb=" N LEU H 107 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 139 removed outlier: 3.739A pdb=" N VAL H 123 " --> pdb=" O ASN H 119 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS H 126 " --> pdb=" O ASN H 122 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET H 127 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU H 129 " --> pdb=" O GLN H 125 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS H 136 " --> pdb=" O VAL H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 171 removed outlier: 4.584A pdb=" N LEU H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR H 171 " --> pdb=" O CYS H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 193 removed outlier: 3.655A pdb=" N LEU H 186 " --> pdb=" O ASN H 182 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE H 187 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN H 192 " --> pdb=" O SER H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 238 removed outlier: 4.490A pdb=" N LYS H 233 " --> pdb=" O THR H 229 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS H 234 " --> pdb=" O GLU H 230 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET H 235 " --> pdb=" O PRO H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 271 removed outlier: 3.625A pdb=" N MET H 268 " --> pdb=" O MET H 264 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY H 269 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 271 " --> pdb=" O PHE H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 298 removed outlier: 3.695A pdb=" N LYS H 297 " --> pdb=" O ASN H 293 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU H 298 " --> pdb=" O CYS H 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 313 removed outlier: 4.320A pdb=" N LYS I 294 " --> pdb=" O ASN I 290 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL I 295 " --> pdb=" O GLN I 291 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN I 313 " --> pdb=" O MET I 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 313 removed outlier: 3.962A pdb=" N LYS J 294 " --> pdb=" O ASN J 290 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL J 295 " --> pdb=" O GLN J 291 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE J 296 " --> pdb=" O TYR J 292 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU J 300 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU J 301 " --> pdb=" O LEU J 297 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN J 313 " --> pdb=" O MET J 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'L' and resid 22 through 34 Processing helix chain 'L' and resid 55 through 60 Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 56 through 60 Processing helix chain 'O' and resid 22 through 35 Processing helix chain 'O' and resid 37 through 41 Processing helix chain 'P' and resid 22 through 35 Processing helix chain 'P' and resid 37 through 39 No H-bonds generated for 'chain 'P' and resid 37 through 39' Processing helix chain 'P' and resid 55 through 60 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.595A pdb=" N ASN C 24 " --> pdb=" O PHE C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.664A pdb=" N LYS C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.848A pdb=" N SER C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 198 removed outlier: 3.599A pdb=" N HIS C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 257 removed outlier: 3.785A pdb=" N HIS C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 93 through 99 removed outlier: 4.128A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 225 through 252 removed outlier: 3.509A pdb=" N VAL A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 257 through 279 Processing helix chain 'A' and resid 279 through 316 Processing helix chain 'B' and resid 16 through 27 removed outlier: 3.532A pdb=" N VAL B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 112 removed outlier: 3.612A pdb=" N THR B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 146 removed outlier: 3.548A pdb=" N MET B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET B 145 " --> pdb=" O MET B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.530A pdb=" N VAL B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 253 removed outlier: 4.135A pdb=" N LYS B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 279 Processing helix chain 'B' and resid 279 through 315 removed outlier: 3.523A pdb=" N GLN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 166 through 169 removed outlier: 9.049A pdb=" N VAL D 167 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA D 8 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA D 169 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU D 10 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 5 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER D 11 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N LYS D 63 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP D 52 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU D 34 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR D 64 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE D 32 " --> pdb=" O TYR D 64 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLU D 30 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 98 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY D 35 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL D 96 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N VAL D 131 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL D 97 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU D 133 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP D 99 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N LEU D 135 " --> pdb=" O TRP D 99 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS D 101 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 150 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS B 172 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 166 through 169 removed outlier: 9.049A pdb=" N VAL D 167 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA D 8 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA D 169 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU D 10 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 5 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER D 11 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N LYS D 63 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP D 52 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU D 34 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR D 64 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE D 32 " --> pdb=" O TYR D 64 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLU D 30 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 98 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY D 35 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL D 96 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N VAL D 131 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL D 97 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU D 133 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP D 99 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N LEU D 135 " --> pdb=" O TRP D 99 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS D 101 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 150 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG B 167 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE B 157 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP B 120 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS B 156 " --> pdb=" O HIS B 124 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS B 38 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP B 120 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY B 36 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N MET B 35 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE B 79 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 37 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL B 77 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE B 39 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 43 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 71 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA B 11 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE B 74 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS B 13 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N SER B 76 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLU B 15 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE B 78 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 12 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 219 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 14 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.417A pdb=" N VAL H 82 " --> pdb=" O ASN J 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 36 through 41 removed outlier: 6.499A pdb=" N ILE E 37 " --> pdb=" O HIS E 59 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N HIS E 59 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP E 39 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS E 57 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 55 " --> pdb=" O LYS E 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 172 through 176 removed outlier: 3.576A pdb=" N SER E 206 " --> pdb=" O TYR E 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 288 through 289 removed outlier: 4.023A pdb=" N ASP E 313 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 36 through 37 removed outlier: 3.725A pdb=" N ARG F 36 " --> pdb=" O HIS F 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 155 through 158 Processing sheet with id=AA9, first strand: chain 'F' and resid 286 through 289 removed outlier: 6.892A pdb=" N THR F 298 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR F 289 " --> pdb=" O LYS F 296 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS F 296 " --> pdb=" O TYR F 289 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP F 313 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR F 324 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 94 through 100 removed outlier: 7.025A pdb=" N VAL G 95 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL G 147 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE G 97 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL G 149 " --> pdb=" O ILE G 97 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU G 99 " --> pdb=" O VAL G 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 211 through 213 removed outlier: 3.997A pdb=" N PHE G 242 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 216 through 217 removed outlier: 6.295A pdb=" N VAL G 245 " --> pdb=" O TYR G 280 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL G 282 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR G 247 " --> pdb=" O VAL G 282 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 153 through 155 removed outlier: 5.410A pdb=" N GLU H 93 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA H 145 " --> pdb=" O GLU H 93 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL H 95 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL H 147 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE H 97 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL H 149 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU H 99 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS H 94 " --> pdb=" O ARG H 212 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE H 214 " --> pdb=" O LYS H 94 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE H 96 " --> pdb=" O ILE H 214 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL H 216 " --> pdb=" O ILE H 96 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS H 98 " --> pdb=" O VAL H 216 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL H 211 " --> pdb=" O PHE H 242 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N ASP H 244 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR H 213 " --> pdb=" O ASP H 244 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL H 246 " --> pdb=" O THR H 213 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU H 215 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE H 248 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR H 217 " --> pdb=" O ILE H 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 273 through 275 Processing sheet with id=AB6, first strand: chain 'K' and resid 13 through 16 removed outlier: 8.972A pdb=" N LEU K 67 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 12 through 16 Processing sheet with id=AB8, first strand: chain 'L' and resid 73 through 75 removed outlier: 4.585A pdb=" N LEU L 73 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'M' and resid 44 through 45 Processing sheet with id=AC2, first strand: chain 'N' and resid 13 through 16 removed outlier: 3.504A pdb=" N ARG N 42 " --> pdb=" O VAL N 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 12 through 16 Processing sheet with id=AC4, first strand: chain 'P' and resid 12 through 16 Processing sheet with id=AC5, first strand: chain 'C' and resid 166 through 169 removed outlier: 6.675A pdb=" N SER C 7 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE C 61 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 9 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LYS C 63 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N SER C 11 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 13.184A pdb=" N ILE C 65 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE C 59 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS C 38 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE C 61 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU C 36 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU C 30 " --> pdb=" O CYS C 67 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 29 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 98 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY C 35 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL C 96 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N VAL C 131 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL C 97 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU C 133 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP C 99 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU C 135 " --> pdb=" O TRP C 99 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS C 101 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 150 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 210 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 166 through 169 removed outlier: 6.675A pdb=" N SER C 7 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE C 61 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 9 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LYS C 63 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N SER C 11 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 13.184A pdb=" N ILE C 65 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE C 59 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS C 38 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE C 61 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU C 36 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU C 30 " --> pdb=" O CYS C 67 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 29 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 98 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY C 35 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL C 96 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N VAL C 131 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL C 97 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU C 133 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP C 99 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU C 135 " --> pdb=" O TRP C 99 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS C 101 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 150 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 165 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU A 159 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ARG A 167 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE A 157 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N VAL A 150 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A 118 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU A 152 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP A 120 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N PHE A 154 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N HIS A 122 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N CYS A 156 " --> pdb=" O HIS A 122 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS A 38 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TRP A 120 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY A 36 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N MET A 35 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE A 79 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 37 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 77 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE A 39 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER A 76 " --> pdb=" O GLU A 15 " (cutoff:3.500A) 1002 hydrogen bonds defined for protein. 2857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5874 1.33 - 1.45: 4463 1.45 - 1.57: 13632 1.57 - 1.70: 0 1.70 - 1.82: 190 Bond restraints: 24159 Sorted by residual: bond pdb=" N PHE G 241 " pdb=" CA PHE G 241 " ideal model delta sigma weight residual 1.457 1.502 -0.046 1.24e-02 6.50e+03 1.37e+01 bond pdb=" CA SER D 143 " pdb=" CB SER D 143 " ideal model delta sigma weight residual 1.528 1.480 0.047 1.35e-02 5.49e+03 1.22e+01 bond pdb=" N LEU B 235 " pdb=" CA LEU B 235 " ideal model delta sigma weight residual 1.462 1.488 -0.026 7.70e-03 1.69e+04 1.17e+01 bond pdb=" N ILE J 280 " pdb=" CA ILE J 280 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.01e-02 9.80e+03 1.01e+01 bond pdb=" N TYR C 179 " pdb=" CA TYR C 179 " ideal model delta sigma weight residual 1.453 1.490 -0.036 1.27e-02 6.20e+03 8.13e+00 ... (remaining 24154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 32099 2.46 - 4.93: 486 4.93 - 7.39: 73 7.39 - 9.85: 19 9.85 - 12.32: 4 Bond angle restraints: 32681 Sorted by residual: angle pdb=" N LYS D 158 " pdb=" CA LYS D 158 " pdb=" CB LYS D 158 " ideal model delta sigma weight residual 110.57 102.82 7.75 1.35e+00 5.49e-01 3.30e+01 angle pdb=" CA GLY C 159 " pdb=" C GLY C 159 " pdb=" O GLY C 159 " ideal model delta sigma weight residual 122.24 117.71 4.53 8.70e-01 1.32e+00 2.72e+01 angle pdb=" N VAL D 14 " pdb=" CA VAL D 14 " pdb=" C VAL D 14 " ideal model delta sigma weight residual 112.96 108.21 4.75 1.00e+00 1.00e+00 2.26e+01 angle pdb=" CA LYS D 158 " pdb=" C LYS D 158 " pdb=" O LYS D 158 " ideal model delta sigma weight residual 122.37 117.18 5.19 1.15e+00 7.56e-01 2.04e+01 angle pdb=" CA TYR G 240 " pdb=" C TYR G 240 " pdb=" O TYR G 240 " ideal model delta sigma weight residual 120.65 115.13 5.52 1.23e+00 6.61e-01 2.01e+01 ... (remaining 32676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12908 17.94 - 35.89: 1336 35.89 - 53.83: 365 53.83 - 71.78: 75 71.78 - 89.72: 23 Dihedral angle restraints: 14707 sinusoidal: 6069 harmonic: 8638 Sorted by residual: dihedral pdb=" CD ARG I 312 " pdb=" NE ARG I 312 " pdb=" CZ ARG I 312 " pdb=" NH1 ARG I 312 " ideal model delta sinusoidal sigma weight residual 0.00 -41.14 41.14 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CA VAL G 245 " pdb=" C VAL G 245 " pdb=" N VAL G 246 " pdb=" CA VAL G 246 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLU G 230 " pdb=" C GLU G 230 " pdb=" N PRO G 231 " pdb=" CA PRO G 231 " ideal model delta harmonic sigma weight residual -180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 14704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3039 0.056 - 0.111: 516 0.111 - 0.167: 85 0.167 - 0.223: 13 0.223 - 0.278: 3 Chirality restraints: 3656 Sorted by residual: chirality pdb=" CA GLU M 64 " pdb=" N GLU M 64 " pdb=" C GLU M 64 " pdb=" CB GLU M 64 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PRO D 156 " pdb=" N PRO D 156 " pdb=" C PRO D 156 " pdb=" CB PRO D 156 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE B 176 " pdb=" N ILE B 176 " pdb=" C ILE B 176 " pdb=" CB ILE B 176 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3653 not shown) Planarity restraints: 4223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 312 " -0.722 9.50e-02 1.11e+02 3.24e-01 6.39e+01 pdb=" NE ARG I 312 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG I 312 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG I 312 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 312 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 224 " -0.479 9.50e-02 1.11e+02 2.15e-01 2.83e+01 pdb=" NE ARG E 224 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG E 224 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 224 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 224 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 9 " -0.478 9.50e-02 1.11e+02 2.14e-01 2.82e+01 pdb=" NE ARG F 9 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG F 9 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG F 9 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 9 " -0.017 2.00e-02 2.50e+03 ... (remaining 4220 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.73: 7 1.73 - 2.53: 194 2.53 - 3.32: 26479 3.32 - 4.11: 54307 4.11 - 4.90: 98151 Warning: very small nonbonded interaction distances. Nonbonded interactions: 179138 Sorted by model distance: nonbonded pdb=" CE MET H 105 " pdb=" CB ALA H 120 " model vdw 0.942 3.880 nonbonded pdb=" OE1 GLN C 176 " pdb=" OE2 GLU A 32 " model vdw 1.432 3.040 nonbonded pdb=" OE1 GLN F 344 " pdb=" OH TYR F 365 " model vdw 1.556 3.040 nonbonded pdb=" CG2 VAL H 245 " pdb=" CE MET H 268 " model vdw 1.593 3.880 nonbonded pdb=" CD1 LEU H 146 " pdb=" CD2 LEU H 166 " model vdw 1.605 3.880 ... (remaining 179133 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 9 through 72 or resid 74 through 178 or resid 211 through \ 401)) selection = (chain 'B' and (resid 9 through 72 or resid 74 through 401)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 4 through 40 or resid 55 through 184 or (resid 185 and (na \ me N or name CA or name C or name O or name CB )) or resid 186 through 327)) } ncs_group { reference = (chain 'E' and resid 2 through 381) selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 81 through 316) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and (resid 2 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 75 or (resid 76 and (name N or name \ CA or name C or name O )))) selection = (chain 'L' and (resid 2 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 76)) selection = chain 'M' selection = (chain 'N' and (resid 2 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 76)) selection = (chain 'O' and (resid 2 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 75 or (resid 76 and (name N or name \ CA or name C or name O )))) selection = (chain 'P' and (resid 2 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 75 or (resid 76 and (name N or name \ CA or name C or name O )))) } 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=0.00 max=1.00 mean=0.82 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: 7.380 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.690 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 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 0.407 24167 Z= 0.412 Angle : 0.706 12.318 32681 Z= 0.385 Chirality : 0.045 0.278 3656 Planarity : 0.009 0.324 4223 Dihedral : 15.975 89.724 9099 Min Nonbonded Distance : 0.942 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer: Outliers : 0.38 % Allowed : 23.89 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.16), residues: 2917 helix: 0.40 (0.17), residues: 894 sheet: 0.13 (0.23), residues: 580 loop : -0.45 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 164 TYR 0.023 0.002 TYR H 280 PHE 0.027 0.001 PHE F 240 TRP 0.013 0.001 TRP A 130 HIS 0.007 0.001 HIS D 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.20 (24159) covalent geometry : angle 0.70612 / 0.38 (32681) hydrogen bonds : bond 0.27244 / 18.56 ( 944) hydrogen bonds : angle 8.14882 / 5.74 ( 2857) metal coordination : bond 0.00244 / 0.15 ( 4) Misc. bond : bond 0.27920 / 15.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 702 time to evaluate : 0.856 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: D 38 LYS cc_start: 0.7947 (mttt) cc_final: 0.7613 (mtmm) REVERT: D 40 GLU cc_start: 0.6790 (tt0) cc_final: 0.6524 (tt0) REVERT: D 87 LYS cc_start: 0.7939 (mttt) cc_final: 0.7632 (mttt) REVERT: D 94 LYS cc_start: 0.7569 (mttp) cc_final: 0.7151 (mttm) REVERT: D 108 GLN cc_start: 0.8831 (tp-100) cc_final: 0.8486 (tp40) REVERT: D 201 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7281 (mtpt) REVERT: D 225 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7722 (mm-30) REVERT: E 170 SER cc_start: 0.8369 (m) cc_final: 0.7955 (t) REVERT: E 172 ARG cc_start: 0.7759 (tpp80) cc_final: 0.7344 (ttp80) REVERT: F 48 THR cc_start: 0.8332 (m) cc_final: 0.8074 (p) REVERT: F 52 ASN cc_start: 0.8495 (p0) cc_final: 0.8176 (p0) REVERT: F 104 SER cc_start: 0.8435 (m) cc_final: 0.8125 (p) REVERT: F 139 MET cc_start: 0.7757 (ttp) cc_final: 0.7240 (tpp) REVERT: F 208 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7133 (mt-10) REVERT: F 216 TYR cc_start: 0.8063 (m-80) cc_final: 0.7230 (m-10) REVERT: F 252 GLN cc_start: 0.8374 (tt0) cc_final: 0.8039 (tt0) REVERT: C 36 GLU cc_start: 0.7931 (tt0) cc_final: 0.7513 (tt0) REVERT: C 208 SER cc_start: 0.8441 (p) cc_final: 0.8187 (m) REVERT: C 218 MET cc_start: 0.8490 (ttt) cc_final: 0.8162 (ttm) REVERT: C 224 GLU cc_start: 0.7344 (tt0) cc_final: 0.7113 (tt0) REVERT: A 89 ARG cc_start: 0.8657 (mmt-90) cc_final: 0.8284 (mpt180) REVERT: A 103 GLU cc_start: 0.7773 (tp30) cc_final: 0.7392 (tm-30) REVERT: A 109 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7236 (mt-10) REVERT: A 137 ARG cc_start: 0.8263 (tpp80) cc_final: 0.7754 (tpp80) REVERT: B 272 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8025 (mp) outliers start: 10 outliers final: 6 residues processed: 709 average time/residue: 0.5766 time to fit residues: 471.2530 Evaluate side-chains 642 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 635 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 353 TRP Chi-restraints excluded: chain G residue 126 LYS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain B residue 272 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN ** D 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN F 8 ASN I 290 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS A 177 GLN A 285 GLN B 139 GLN B 244 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.174347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150100 restraints weight = 66778.520| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.54 r_work: 0.3703 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4181 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4181 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24167 Z= 0.185 Angle : 0.649 8.300 32681 Z= 0.333 Chirality : 0.045 0.187 3656 Planarity : 0.005 0.053 4223 Dihedral : 4.594 52.774 3181 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.80 % Allowed : 24.79 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.16), residues: 2917 helix: 1.09 (0.16), residues: 973 sheet: 0.11 (0.23), residues: 551 loop : -0.52 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG H 305 TYR 0.022 0.002 TYR H 278 PHE 0.022 0.002 PHE F 369 TRP 0.011 0.001 TRP A 130 HIS 0.009 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (24159) covalent geometry : angle 0.64931 / 0.33 (32681) hydrogen bonds : bond 0.06700 / 4.46 ( 944) hydrogen bonds : angle 5.42912 / 3.85 ( 2857) metal coordination : bond 0.00384 / 0.28 ( 4) Misc. bond : bond 0.00700 / 0.44 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 662 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: D 10 LEU cc_start: 0.7991 (tp) cc_final: 0.7726 (tp) REVERT: D 38 LYS cc_start: 0.7853 (mttt) cc_final: 0.7522 (mtmm) REVERT: D 94 LYS cc_start: 0.7696 (mttp) cc_final: 0.7475 (mttp) REVERT: D 158 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8233 (mtmm) REVERT: D 201 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7413 (mtpt) REVERT: D 321 ASP cc_start: 0.6052 (m-30) cc_final: 0.5765 (m-30) REVERT: E 268 TYR cc_start: 0.8037 (t80) cc_final: 0.7773 (t80) REVERT: F 52 ASN cc_start: 0.8493 (p0) cc_final: 0.8251 (p0) REVERT: F 104 SER cc_start: 0.8323 (m) cc_final: 0.8024 (p) REVERT: F 119 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7317 (mt-10) REVERT: F 139 MET cc_start: 0.8204 (ttp) cc_final: 0.7976 (mmm) REVERT: F 208 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7057 (mt-10) REVERT: F 229 LEU cc_start: 0.8834 (tp) cc_final: 0.8472 (tm) REVERT: C 36 GLU cc_start: 0.8041 (tt0) cc_final: 0.7642 (tt0) REVERT: C 80 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8343 (t) REVERT: C 208 SER cc_start: 0.8505 (p) cc_final: 0.8218 (m) REVERT: C 218 MET cc_start: 0.8290 (ttt) cc_final: 0.8012 (ttm) REVERT: C 224 GLU cc_start: 0.7591 (tt0) cc_final: 0.7375 (tt0) REVERT: A 95 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: A 103 GLU cc_start: 0.7751 (tp30) cc_final: 0.7417 (tm-30) REVERT: A 137 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7623 (tpp80) REVERT: A 209 TYR cc_start: 0.7595 (m-80) cc_final: 0.7349 (m-80) REVERT: A 272 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7971 (mp) REVERT: B 272 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8030 (mp) outliers start: 128 outliers final: 62 residues processed: 727 average time/residue: 0.5809 time to fit residues: 486.3930 Evaluate side-chains 697 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 630 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 353 TRP Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 236 PHE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 200 GLU Chi-restraints excluded: chain H residue 238 CYS Chi-restraints excluded: chain H residue 270 SER Chi-restraints excluded: chain H residue 279 LYS Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 322 GLU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 277 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 12 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 93 optimal weight: 0.0060 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 180 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN F 109 ASN I 290 ASN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 143 GLN A 177 GLN A 244 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.175149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152101 restraints weight = 48332.383| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.94 r_work: 0.3754 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4181 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4181 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24167 Z= 0.148 Angle : 0.608 9.103 32681 Z= 0.308 Chirality : 0.043 0.165 3656 Planarity : 0.004 0.056 4223 Dihedral : 4.305 51.750 3168 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.99 % Allowed : 25.51 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2917 helix: 1.43 (0.17), residues: 971 sheet: 0.08 (0.23), residues: 555 loop : -0.51 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 320 TYR 0.027 0.002 TYR J 292 PHE 0.016 0.002 PHE F 317 TRP 0.010 0.001 TRP A 130 HIS 0.010 0.001 HIS C 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (24159) covalent geometry : angle 0.60782 / 0.31 (32681) hydrogen bonds : bond 0.05906 / 3.95 ( 944) hydrogen bonds : angle 5.00890 / 3.55 ( 2857) metal coordination : bond 0.00320 / 0.24 ( 4) Misc. bond : bond 0.00804 / 0.50 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 658 time to evaluate : 0.898 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: D 38 LYS cc_start: 0.7808 (mttt) cc_final: 0.7480 (mtmm) REVERT: D 40 GLU cc_start: 0.6674 (tt0) cc_final: 0.6371 (tt0) REVERT: D 87 LYS cc_start: 0.7762 (mttt) cc_final: 0.7511 (mmtt) REVERT: D 94 LYS cc_start: 0.7667 (mttp) cc_final: 0.7419 (mmtp) REVERT: D 142 GLU cc_start: 0.8322 (tp30) cc_final: 0.8120 (tp30) REVERT: D 158 LYS cc_start: 0.8473 (mtmm) cc_final: 0.8113 (mtmm) REVERT: D 201 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7402 (mtpt) REVERT: D 225 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7426 (mm-30) REVERT: E 38 THR cc_start: 0.8310 (p) cc_final: 0.8044 (t) REVERT: E 170 SER cc_start: 0.8397 (m) cc_final: 0.7958 (t) REVERT: E 180 ASP cc_start: 0.7927 (t0) cc_final: 0.7657 (t0) REVERT: E 268 TYR cc_start: 0.7927 (t80) cc_final: 0.7662 (t80) REVERT: E 270 LYS cc_start: 0.8733 (tptt) cc_final: 0.8533 (tppp) REVERT: E 340 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7046 (t80) REVERT: F 52 ASN cc_start: 0.8467 (p0) cc_final: 0.8212 (p0) REVERT: F 104 SER cc_start: 0.8305 (m) cc_final: 0.8000 (p) REVERT: F 208 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7020 (mt-10) REVERT: F 229 LEU cc_start: 0.8772 (tp) cc_final: 0.8402 (tm) REVERT: C 36 GLU cc_start: 0.7949 (tt0) cc_final: 0.7549 (tt0) REVERT: C 80 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8321 (t) REVERT: C 208 SER cc_start: 0.8507 (p) cc_final: 0.8224 (m) REVERT: C 218 MET cc_start: 0.8226 (ttt) cc_final: 0.7934 (ttm) REVERT: C 224 GLU cc_start: 0.7556 (tt0) cc_final: 0.7310 (tt0) REVERT: A 95 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: A 103 GLU cc_start: 0.7727 (tp30) cc_final: 0.7324 (tm-30) REVERT: A 137 ARG cc_start: 0.8029 (tpp80) cc_final: 0.7558 (tpp80) REVERT: A 272 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7887 (mp) REVERT: B 144 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7715 (mpt) REVERT: B 272 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7905 (mp) outliers start: 133 outliers final: 65 residues processed: 722 average time/residue: 0.5945 time to fit residues: 494.2375 Evaluate side-chains 709 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 637 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 340 TYR Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 236 PHE Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 238 CYS Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 298 CYS Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 309 MET Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 277 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 227 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 191 optimal weight: 0.4980 chunk 286 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 148 optimal weight: 9.9990 chunk 274 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 236 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN D 162 HIS F 8 ASN F 74 ASN F 101 ASN F 109 ASN I 311 GLN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 143 GLN A 177 GLN A 244 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148870 restraints weight = 60836.087| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.36 r_work: 0.3741 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4181 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24167 Z= 0.133 Angle : 0.602 8.999 32681 Z= 0.302 Chirality : 0.043 0.197 3656 Planarity : 0.004 0.058 4223 Dihedral : 4.144 50.830 3166 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.88 % Allowed : 25.96 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 2917 helix: 1.56 (0.17), residues: 974 sheet: 0.08 (0.23), residues: 552 loop : -0.52 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 320 TYR 0.032 0.002 TYR J 292 PHE 0.036 0.001 PHE G 187 TRP 0.014 0.001 TRP F 353 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (24159) covalent geometry : angle 0.60163 / 0.30 (32681) hydrogen bonds : bond 0.05266 / 3.51 ( 944) hydrogen bonds : angle 4.76292 / 3.38 ( 2857) metal coordination : bond 0.00269 / 0.20 ( 4) Misc. bond : bond 0.00160 / 0.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 643 time to evaluate : 0.865 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: D 38 LYS cc_start: 0.7785 (mttt) cc_final: 0.7442 (mtmm) REVERT: D 40 GLU cc_start: 0.6697 (tt0) cc_final: 0.6401 (tt0) REVERT: D 46 THR cc_start: 0.7264 (p) cc_final: 0.7012 (p) REVERT: D 87 LYS cc_start: 0.7735 (mttt) cc_final: 0.7497 (mmtt) REVERT: D 94 LYS cc_start: 0.7693 (mttp) cc_final: 0.7434 (mmtp) REVERT: D 158 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8042 (mtmm) REVERT: D 201 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7420 (mtpt) REVERT: E 170 SER cc_start: 0.8402 (m) cc_final: 0.7949 (t) REVERT: E 180 ASP cc_start: 0.7970 (t0) cc_final: 0.7695 (t0) REVERT: E 268 TYR cc_start: 0.7937 (t80) cc_final: 0.7601 (t80) REVERT: E 270 LYS cc_start: 0.8779 (tptt) cc_final: 0.8571 (tppp) REVERT: F 52 ASN cc_start: 0.8495 (p0) cc_final: 0.8248 (p0) REVERT: F 104 SER cc_start: 0.8334 (m) cc_final: 0.8022 (p) REVERT: F 183 ASN cc_start: 0.8457 (m110) cc_final: 0.8187 (m-40) REVERT: F 208 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7054 (mt-10) REVERT: F 229 LEU cc_start: 0.8771 (tp) cc_final: 0.8408 (tm) REVERT: J 292 TYR cc_start: 0.7115 (t80) cc_final: 0.6878 (t80) REVERT: C 21 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: C 36 GLU cc_start: 0.7946 (tt0) cc_final: 0.7534 (tt0) REVERT: C 80 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8293 (t) REVERT: C 208 SER cc_start: 0.8524 (p) cc_final: 0.8251 (m) REVERT: C 218 MET cc_start: 0.8234 (ttt) cc_final: 0.7932 (ttm) REVERT: C 224 GLU cc_start: 0.7595 (tt0) cc_final: 0.7340 (tt0) REVERT: A 70 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7216 (mtp-110) REVERT: A 86 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7276 (ttm-80) REVERT: A 95 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: A 103 GLU cc_start: 0.7765 (tp30) cc_final: 0.7332 (tm-30) REVERT: A 137 ARG cc_start: 0.8024 (tpp80) cc_final: 0.7538 (tpp80) REVERT: A 209 TYR cc_start: 0.7684 (m-80) cc_final: 0.7383 (m-80) REVERT: A 272 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7917 (mp) REVERT: B 144 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7730 (mpt) REVERT: B 272 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7900 (mp) outliers start: 130 outliers final: 70 residues processed: 693 average time/residue: 0.5938 time to fit residues: 473.2412 Evaluate side-chains 697 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 621 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 236 PHE Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 267 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 238 CYS Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 298 CYS Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 309 MET Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 277 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 45 optimal weight: 2.9990 chunk 92 optimal weight: 0.0020 chunk 48 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN F 8 ASN F 109 ASN J 299 GLN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.172847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148066 restraints weight = 77433.512| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.88 r_work: 0.3700 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24167 Z= 0.150 Angle : 0.624 10.918 32681 Z= 0.310 Chirality : 0.044 0.210 3656 Planarity : 0.004 0.058 4223 Dihedral : 4.173 50.900 3166 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.25 % Allowed : 25.58 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.16), residues: 2917 helix: 1.63 (0.17), residues: 973 sheet: 0.05 (0.23), residues: 546 loop : -0.55 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 320 TYR 0.032 0.002 TYR J 292 PHE 0.025 0.002 PHE G 187 TRP 0.010 0.001 TRP G 155 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (24159) covalent geometry : angle 0.62365 / 0.31 (32681) hydrogen bonds : bond 0.05221 / 3.48 ( 944) hydrogen bonds : angle 4.68634 / 3.33 ( 2857) metal coordination : bond 0.00377 / 0.28 ( 4) Misc. bond : bond 0.00147 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 638 time to evaluate : 0.866 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: D 9 VAL cc_start: 0.8315 (t) cc_final: 0.7775 (p) REVERT: D 38 LYS cc_start: 0.7812 (mttt) cc_final: 0.7464 (mtmm) REVERT: D 87 LYS cc_start: 0.7708 (mttt) cc_final: 0.7476 (mmtt) REVERT: D 94 LYS cc_start: 0.7730 (mttp) cc_final: 0.7463 (mmtp) REVERT: D 158 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8104 (mtmm) REVERT: D 201 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7468 (mtpt) REVERT: E 170 SER cc_start: 0.8427 (m) cc_final: 0.7976 (t) REVERT: E 180 ASP cc_start: 0.8033 (t0) cc_final: 0.7791 (t0) REVERT: E 268 TYR cc_start: 0.8016 (t80) cc_final: 0.7693 (t80) REVERT: E 270 LYS cc_start: 0.8831 (tptt) cc_final: 0.8631 (tppp) REVERT: E 340 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7135 (t80) REVERT: F 8 ASN cc_start: 0.8510 (t0) cc_final: 0.8303 (t160) REVERT: F 52 ASN cc_start: 0.8519 (p0) cc_final: 0.8273 (p0) REVERT: F 104 SER cc_start: 0.8390 (m) cc_final: 0.8072 (p) REVERT: F 183 ASN cc_start: 0.8524 (m110) cc_final: 0.8245 (m-40) REVERT: F 208 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7126 (mt-10) REVERT: F 229 LEU cc_start: 0.8818 (tp) cc_final: 0.8450 (tm) REVERT: C 21 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: C 36 GLU cc_start: 0.8019 (tt0) cc_final: 0.7612 (tt0) REVERT: C 80 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8291 (t) REVERT: C 208 SER cc_start: 0.8506 (p) cc_final: 0.8254 (m) REVERT: C 224 GLU cc_start: 0.7682 (tt0) cc_final: 0.7426 (tt0) REVERT: A 70 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7268 (mtp-110) REVERT: A 95 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: A 103 GLU cc_start: 0.7809 (tp30) cc_final: 0.7370 (tm-30) REVERT: A 209 TYR cc_start: 0.7754 (m-80) cc_final: 0.7381 (m-80) REVERT: A 272 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 144 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7745 (mpt) REVERT: B 241 GLN cc_start: 0.7528 (mt0) cc_final: 0.7282 (mm-40) REVERT: B 272 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7958 (mp) outliers start: 140 outliers final: 80 residues processed: 696 average time/residue: 0.5828 time to fit residues: 466.7141 Evaluate side-chains 710 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 622 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 340 TYR Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 236 PHE Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 267 PHE Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 238 CYS Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 298 CYS Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 309 MET Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 277 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 272 optimal weight: 0.0170 chunk 138 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN D 108 GLN ** D 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.172559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.149410 restraints weight = 51834.479| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.03 r_work: 0.3758 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24167 Z= 0.143 Angle : 0.628 10.869 32681 Z= 0.311 Chirality : 0.044 0.221 3656 Planarity : 0.004 0.082 4223 Dihedral : 4.100 50.692 3164 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.80 % Allowed : 27.16 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.16), residues: 2917 helix: 1.65 (0.17), residues: 968 sheet: 0.08 (0.23), residues: 543 loop : -0.56 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 320 TYR 0.038 0.002 TYR J 292 PHE 0.020 0.001 PHE G 187 TRP 0.010 0.001 TRP G 155 HIS 0.008 0.001 HIS C 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (24159) covalent geometry : angle 0.62822 / 0.31 (32681) hydrogen bonds : bond 0.05019 / 3.35 ( 944) hydrogen bonds : angle 4.59393 / 3.26 ( 2857) metal coordination : bond 0.00343 / 0.26 ( 4) Misc. bond : bond 0.00125 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 633 time to evaluate : 0.907 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: D 9 VAL cc_start: 0.8259 (t) cc_final: 0.7731 (p) REVERT: D 38 LYS cc_start: 0.7735 (mttt) cc_final: 0.7373 (mtmm) REVERT: D 87 LYS cc_start: 0.7705 (mttt) cc_final: 0.7477 (mmtt) REVERT: D 94 LYS cc_start: 0.7681 (mttp) cc_final: 0.7410 (mmtp) REVERT: D 142 GLU cc_start: 0.8185 (tp30) cc_final: 0.7984 (tp30) REVERT: D 155 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8046 (tttt) REVERT: D 158 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7905 (mtmm) REVERT: D 201 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7385 (mtpt) REVERT: D 225 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7414 (mm-30) REVERT: E 170 SER cc_start: 0.8384 (m) cc_final: 0.7915 (t) REVERT: E 270 LYS cc_start: 0.8820 (tptt) cc_final: 0.8593 (tppp) REVERT: E 340 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7083 (t80) REVERT: F 8 ASN cc_start: 0.8487 (t0) cc_final: 0.8240 (t160) REVERT: F 52 ASN cc_start: 0.8493 (p0) cc_final: 0.8242 (p0) REVERT: F 104 SER cc_start: 0.8374 (m) cc_final: 0.8050 (p) REVERT: F 183 ASN cc_start: 0.8462 (m110) cc_final: 0.8179 (m-40) REVERT: F 208 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7038 (mt-10) REVERT: F 229 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8428 (tm) REVERT: C 21 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: C 36 GLU cc_start: 0.7913 (tt0) cc_final: 0.7498 (tt0) REVERT: C 80 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8246 (t) REVERT: C 208 SER cc_start: 0.8458 (p) cc_final: 0.8216 (m) REVERT: C 224 GLU cc_start: 0.7579 (tt0) cc_final: 0.7323 (tt0) REVERT: A 70 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7187 (mtp-110) REVERT: A 95 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 103 GLU cc_start: 0.7691 (tp30) cc_final: 0.7230 (tm-30) REVERT: A 272 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7847 (mp) REVERT: B 144 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7703 (mpt) REVERT: B 241 GLN cc_start: 0.7393 (mt0) cc_final: 0.7165 (mm-40) REVERT: B 272 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7846 (mp) outliers start: 128 outliers final: 77 residues processed: 687 average time/residue: 0.6021 time to fit residues: 475.4700 Evaluate side-chains 703 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 616 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 340 TYR Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 236 PHE Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 267 PHE Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 238 CYS Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 298 CYS Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 277 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 21 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 203 optimal weight: 0.0060 chunk 104 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 269 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 148 optimal weight: 9.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN D 108 GLN E 183 ASN F 109 ASN F 183 ASN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.172126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.148565 restraints weight = 57636.551| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.24 r_work: 0.3734 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24167 Z= 0.161 Angle : 0.653 11.501 32681 Z= 0.324 Chirality : 0.044 0.235 3656 Planarity : 0.004 0.081 4223 Dihedral : 4.151 50.959 3164 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.65 % Allowed : 27.31 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.16), residues: 2917 helix: 1.66 (0.17), residues: 970 sheet: 0.00 (0.23), residues: 543 loop : -0.60 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 320 TYR 0.045 0.002 TYR J 292 PHE 0.020 0.002 PHE J 320 TRP 0.010 0.001 TRP G 155 HIS 0.008 0.001 HIS C 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (24159) covalent geometry : angle 0.65335 / 0.32 (32681) hydrogen bonds : bond 0.05070 / 3.38 ( 944) hydrogen bonds : angle 4.58601 / 3.25 ( 2857) metal coordination : bond 0.00437 / 0.32 ( 4) Misc. bond : bond 0.00066 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 624 time to evaluate : 0.649 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: D 9 VAL cc_start: 0.8307 (t) cc_final: 0.7782 (p) REVERT: D 38 LYS cc_start: 0.7753 (mttt) cc_final: 0.7428 (mtmm) REVERT: D 87 LYS cc_start: 0.7710 (mttt) cc_final: 0.7481 (mmtt) REVERT: D 94 LYS cc_start: 0.7702 (mttp) cc_final: 0.7404 (mmtp) REVERT: D 155 LYS cc_start: 0.8317 (tppt) cc_final: 0.8049 (tttt) REVERT: D 158 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7833 (mtmm) REVERT: D 201 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7473 (mtpt) REVERT: D 225 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7506 (mm-30) REVERT: E 170 SER cc_start: 0.8438 (m) cc_final: 0.7948 (t) REVERT: E 270 LYS cc_start: 0.8767 (tptt) cc_final: 0.8559 (tppp) REVERT: E 340 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7087 (t80) REVERT: F 52 ASN cc_start: 0.8484 (p0) cc_final: 0.8233 (p0) REVERT: F 104 SER cc_start: 0.8387 (m) cc_final: 0.8073 (p) REVERT: F 208 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7054 (mt-10) REVERT: F 229 LEU cc_start: 0.8780 (tp) cc_final: 0.8418 (tm) REVERT: F 279 LEU cc_start: 0.8194 (mt) cc_final: 0.7970 (mm) REVERT: C 36 GLU cc_start: 0.7961 (tt0) cc_final: 0.7554 (tt0) REVERT: C 80 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8296 (t) REVERT: C 119 LYS cc_start: 0.8396 (mmmm) cc_final: 0.8069 (mmpt) REVERT: C 208 SER cc_start: 0.8494 (p) cc_final: 0.8251 (m) REVERT: C 224 GLU cc_start: 0.7606 (tt0) cc_final: 0.7366 (tt0) REVERT: A 70 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7232 (mtp-110) REVERT: A 95 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 103 GLU cc_start: 0.7744 (tp30) cc_final: 0.7293 (tm-30) REVERT: A 272 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7932 (mp) REVERT: B 144 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7706 (mpt) REVERT: B 241 GLN cc_start: 0.7442 (mt0) cc_final: 0.7229 (mm-40) REVERT: B 272 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7933 (mp) outliers start: 124 outliers final: 87 residues processed: 673 average time/residue: 0.6026 time to fit residues: 466.7894 Evaluate side-chains 715 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 621 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 340 TYR Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 236 PHE Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 267 PHE Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 230 GLU Chi-restraints excluded: chain H residue 238 CYS Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 298 CYS Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 309 MET Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 277 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 71 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 211 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 207 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN D 108 GLN E 183 ASN F 109 ASN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.172616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148799 restraints weight = 73636.803| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.66 r_work: 0.3713 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24167 Z= 0.157 Angle : 0.681 12.211 32681 Z= 0.334 Chirality : 0.044 0.230 3656 Planarity : 0.004 0.080 4223 Dihedral : 4.197 50.662 3164 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.50 % Allowed : 28.21 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 2917 helix: 1.65 (0.17), residues: 969 sheet: -0.03 (0.23), residues: 543 loop : -0.61 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 164 TYR 0.043 0.002 TYR J 292 PHE 0.024 0.002 PHE J 320 TRP 0.010 0.001 TRP E 303 HIS 0.009 0.001 HIS C 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (24159) covalent geometry : angle 0.68143 / 0.33 (32681) hydrogen bonds : bond 0.05002 / 3.33 ( 944) hydrogen bonds : angle 4.56267 / 3.24 ( 2857) metal coordination : bond 0.00389 / 0.29 ( 4) Misc. bond : bond 0.00152 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 623 time to evaluate : 0.845 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: D 9 VAL cc_start: 0.8311 (t) cc_final: 0.7787 (p) REVERT: D 38 LYS cc_start: 0.7786 (mttt) cc_final: 0.7445 (mtmm) REVERT: D 87 LYS cc_start: 0.7680 (mttt) cc_final: 0.7458 (mmtt) REVERT: D 94 LYS cc_start: 0.7730 (mttp) cc_final: 0.7413 (mmtp) REVERT: D 158 LYS cc_start: 0.8393 (mtmm) cc_final: 0.7998 (mtmm) REVERT: D 201 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7498 (mtpt) REVERT: E 57 LYS cc_start: 0.8558 (mttm) cc_final: 0.8346 (mttp) REVERT: E 170 SER cc_start: 0.8439 (m) cc_final: 0.7938 (t) REVERT: E 195 ASP cc_start: 0.7364 (t0) cc_final: 0.6947 (t0) REVERT: E 266 GLN cc_start: 0.8384 (tp40) cc_final: 0.8113 (tp-100) REVERT: E 270 LYS cc_start: 0.8826 (tptt) cc_final: 0.8584 (tppp) REVERT: E 340 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.7123 (t80) REVERT: F 52 ASN cc_start: 0.8508 (p0) cc_final: 0.8252 (p0) REVERT: F 104 SER cc_start: 0.8423 (m) cc_final: 0.8104 (p) REVERT: F 208 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7104 (mt-10) REVERT: F 216 TYR cc_start: 0.8272 (m-80) cc_final: 0.7193 (m-80) REVERT: F 229 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8462 (tm) REVERT: F 279 LEU cc_start: 0.8253 (mt) cc_final: 0.8030 (mm) REVERT: I 312 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7819 (mmp-170) REVERT: C 21 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: C 36 GLU cc_start: 0.7991 (tt0) cc_final: 0.7574 (tt0) REVERT: C 80 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8274 (t) REVERT: C 101 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7360 (tptt) REVERT: C 119 LYS cc_start: 0.8422 (mmmm) cc_final: 0.8074 (mmpt) REVERT: C 208 SER cc_start: 0.8476 (p) cc_final: 0.8244 (m) REVERT: C 218 MET cc_start: 0.8246 (ttp) cc_final: 0.7946 (ttm) REVERT: C 224 GLU cc_start: 0.7677 (tt0) cc_final: 0.7417 (tt0) REVERT: A 70 ARG cc_start: 0.7602 (mtt180) cc_final: 0.7232 (mtp-110) REVERT: A 86 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7225 (ttm-80) REVERT: A 95 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: A 103 GLU cc_start: 0.7768 (tp30) cc_final: 0.7331 (tm-30) REVERT: A 207 GLU cc_start: 0.7312 (mp0) cc_final: 0.7109 (mp0) REVERT: A 209 TYR cc_start: 0.7667 (m-80) cc_final: 0.7382 (m-80) REVERT: A 272 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7923 (mp) REVERT: B 144 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7718 (mpt) REVERT: B 241 GLN cc_start: 0.7440 (mt0) cc_final: 0.7219 (mm-40) REVERT: B 272 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7922 (mp) outliers start: 120 outliers final: 82 residues processed: 672 average time/residue: 0.5959 time to fit residues: 459.9238 Evaluate side-chains 710 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 617 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 278 PHE Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 340 TYR Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 236 PHE Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 267 PHE Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 238 CYS Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 298 CYS Chi-restraints excluded: chain I residue 312 ARG Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 277 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 221 optimal weight: 0.3980 chunk 133 optimal weight: 0.8980 chunk 119 optimal weight: 0.0970 chunk 195 optimal weight: 0.2980 chunk 287 optimal weight: 1.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN D 108 GLN E 183 ASN F 101 ASN F 109 ASN F 150 GLN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.173315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151077 restraints weight = 42505.339| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.73 r_work: 0.3794 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24167 Z= 0.131 Angle : 0.698 13.041 32681 Z= 0.339 Chirality : 0.044 0.226 3656 Planarity : 0.004 0.082 4223 Dihedral : 4.138 49.474 3164 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.53 % Allowed : 29.82 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.16), residues: 2917 helix: 1.70 (0.17), residues: 956 sheet: 0.01 (0.23), residues: 559 loop : -0.58 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 320 TYR 0.041 0.002 TYR J 292 PHE 0.034 0.001 PHE F 240 TRP 0.010 0.001 TRP A 130 HIS 0.013 0.001 HIS H 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (24159) covalent geometry : angle 0.69782 / 0.34 (32681) hydrogen bonds : bond 0.04679 / 3.12 ( 944) hydrogen bonds : angle 4.50995 / 3.20 ( 2857) metal coordination : bond 0.00221 / 0.17 ( 4) Misc. bond : bond 0.00056 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 621 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 9 VAL cc_start: 0.8270 (t) cc_final: 0.7751 (p) REVERT: D 38 LYS cc_start: 0.7728 (mttt) cc_final: 0.7408 (mtmm) REVERT: D 46 THR cc_start: 0.7277 (p) cc_final: 0.7037 (p) REVERT: D 87 LYS cc_start: 0.7714 (mttt) cc_final: 0.7485 (mmtt) REVERT: D 94 LYS cc_start: 0.7643 (mttp) cc_final: 0.7370 (mmtp) REVERT: D 155 LYS cc_start: 0.8271 (tttt) cc_final: 0.8067 (tttt) REVERT: D 158 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7875 (mtmm) REVERT: D 201 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7395 (mtpt) REVERT: E 170 SER cc_start: 0.8404 (m) cc_final: 0.7925 (t) REVERT: E 188 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7717 (mt) REVERT: E 195 ASP cc_start: 0.7187 (t0) cc_final: 0.6757 (t0) REVERT: E 266 GLN cc_start: 0.8225 (tp40) cc_final: 0.7931 (tp-100) REVERT: E 270 LYS cc_start: 0.8733 (tptt) cc_final: 0.8501 (tppp) REVERT: F 48 THR cc_start: 0.8403 (m) cc_final: 0.8140 (p) REVERT: F 52 ASN cc_start: 0.8462 (p0) cc_final: 0.8136 (p0) REVERT: F 104 SER cc_start: 0.8351 (m) cc_final: 0.8038 (p) REVERT: F 208 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6979 (mt-10) REVERT: F 216 TYR cc_start: 0.8228 (m-80) cc_final: 0.7037 (m-80) REVERT: F 229 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8380 (tm) REVERT: F 240 PHE cc_start: 0.7115 (t80) cc_final: 0.6879 (t80) REVERT: F 279 LEU cc_start: 0.8163 (mt) cc_final: 0.7937 (mm) REVERT: I 312 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7727 (mmp-170) REVERT: C 21 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: C 36 GLU cc_start: 0.7881 (tt0) cc_final: 0.7464 (tt0) REVERT: C 101 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7360 (tptt) REVERT: C 119 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8046 (mmpt) REVERT: C 208 SER cc_start: 0.8480 (p) cc_final: 0.8217 (m) REVERT: C 218 MET cc_start: 0.8186 (ttp) cc_final: 0.7894 (ttm) REVERT: C 224 GLU cc_start: 0.7545 (tt0) cc_final: 0.7309 (tt0) REVERT: A 70 ARG cc_start: 0.7499 (mtt180) cc_final: 0.7169 (mtp-110) REVERT: A 86 ARG cc_start: 0.7515 (ttm-80) cc_final: 0.7108 (ttm-80) REVERT: A 95 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 103 GLU cc_start: 0.7719 (tp30) cc_final: 0.7331 (tm-30) REVERT: A 209 TYR cc_start: 0.7597 (m-80) cc_final: 0.7388 (m-80) REVERT: B 144 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7683 (mpt) REVERT: B 241 GLN cc_start: 0.7362 (mt0) cc_final: 0.7158 (mm-40) REVERT: B 272 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7829 (mp) outliers start: 94 outliers final: 68 residues processed: 660 average time/residue: 0.5995 time to fit residues: 454.9530 Evaluate side-chains 686 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 609 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 278 PHE Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 236 PHE Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 267 PHE Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 230 GLU Chi-restraints excluded: chain H residue 238 CYS Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 279 LYS Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 312 ARG Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 277 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 202 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 235 optimal weight: 8.9990 chunk 241 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 0.0170 chunk 40 optimal weight: 0.0010 chunk 239 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 overall best weight: 0.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN D 108 GLN F 101 ASN F 109 ASN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.173920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.150665 restraints weight = 55698.364| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 3.17 r_work: 0.3768 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24167 Z= 0.131 Angle : 0.709 12.619 32681 Z= 0.344 Chirality : 0.044 0.210 3656 Planarity : 0.004 0.084 4223 Dihedral : 4.158 48.795 3164 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.19 % Allowed : 30.27 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.16), residues: 2917 helix: 1.72 (0.17), residues: 947 sheet: -0.00 (0.23), residues: 559 loop : -0.58 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 320 TYR 0.036 0.002 TYR J 292 PHE 0.025 0.001 PHE F 240 TRP 0.010 0.001 TRP E 303 HIS 0.016 0.001 HIS C 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (24159) covalent geometry : angle 0.70931 / 0.34 (32681) hydrogen bonds : bond 0.04544 / 3.04 ( 944) hydrogen bonds : angle 4.45578 / 3.17 ( 2857) metal coordination : bond 0.00207 / 0.16 ( 4) Misc. bond : bond 0.00042 / 0.03 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 624 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 9 VAL cc_start: 0.8288 (t) cc_final: 0.7735 (p) REVERT: D 38 LYS cc_start: 0.7752 (mttt) cc_final: 0.7423 (mtmm) REVERT: D 46 THR cc_start: 0.7272 (p) cc_final: 0.7027 (p) REVERT: D 87 LYS cc_start: 0.7696 (mttt) cc_final: 0.7470 (mmtt) REVERT: D 94 LYS cc_start: 0.7660 (mttp) cc_final: 0.7396 (mmtp) REVERT: D 158 LYS cc_start: 0.8368 (mtmm) cc_final: 0.7899 (mtmm) REVERT: D 201 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7412 (mtpt) REVERT: E 34 CYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7666 (p) REVERT: E 170 SER cc_start: 0.8431 (m) cc_final: 0.7930 (t) REVERT: E 188 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7784 (mt) REVERT: E 195 ASP cc_start: 0.7214 (t0) cc_final: 0.6816 (t0) REVERT: E 266 GLN cc_start: 0.8202 (tp40) cc_final: 0.7899 (tp-100) REVERT: E 270 LYS cc_start: 0.8745 (tptt) cc_final: 0.8516 (tppp) REVERT: F 48 THR cc_start: 0.8399 (m) cc_final: 0.8131 (p) REVERT: F 52 ASN cc_start: 0.8493 (p0) cc_final: 0.8164 (p0) REVERT: F 104 SER cc_start: 0.8376 (m) cc_final: 0.8060 (p) REVERT: F 208 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7053 (mt-10) REVERT: F 216 TYR cc_start: 0.8273 (m-80) cc_final: 0.7129 (m-80) REVERT: F 229 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8355 (tm) REVERT: F 240 PHE cc_start: 0.7175 (t80) cc_final: 0.6906 (t80) REVERT: F 252 GLN cc_start: 0.8274 (tt0) cc_final: 0.7979 (tt0) REVERT: F 279 LEU cc_start: 0.8193 (mt) cc_final: 0.7963 (mm) REVERT: I 312 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7722 (mmp-170) REVERT: C 21 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: C 36 GLU cc_start: 0.7916 (tt0) cc_final: 0.7500 (tt0) REVERT: C 101 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.7346 (tptt) REVERT: C 119 LYS cc_start: 0.8395 (mmmm) cc_final: 0.8061 (mmpt) REVERT: C 208 SER cc_start: 0.8494 (p) cc_final: 0.8228 (m) REVERT: C 218 MET cc_start: 0.8193 (ttp) cc_final: 0.7910 (ttm) REVERT: C 224 GLU cc_start: 0.7553 (tt0) cc_final: 0.7287 (tt0) REVERT: C 237 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 86 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7080 (ttm-80) REVERT: A 95 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: A 103 GLU cc_start: 0.7764 (tp30) cc_final: 0.7294 (tm-30) REVERT: A 209 TYR cc_start: 0.7660 (m-80) cc_final: 0.7395 (m-80) REVERT: B 144 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7712 (mpt) REVERT: B 272 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7886 (mp) outliers start: 85 outliers final: 63 residues processed: 660 average time/residue: 0.5938 time to fit residues: 450.9321 Evaluate side-chains 692 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 619 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 278 PHE Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain F residue 133 ARG Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 267 PHE Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 230 GLU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 279 LYS Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 312 ARG Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 309 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 160 optimal weight: 1.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 108 GLN F 109 ASN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN B 139 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.172730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149128 restraints weight = 66959.694| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.52 r_work: 0.3731 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4182 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24167 Z= 0.160 Angle : 0.725 11.622 32681 Z= 0.354 Chirality : 0.045 0.209 3656 Planarity : 0.004 0.085 4223 Dihedral : 4.217 49.737 3164 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.96 % Allowed : 30.61 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2917 helix: 1.65 (0.17), residues: 951 sheet: -0.03 (0.23), residues: 545 loop : -0.61 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 164 TYR 0.035 0.002 TYR J 292 PHE 0.029 0.002 PHE C 288 TRP 0.010 0.001 TRP F 303 HIS 0.011 0.001 HIS C 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (24159) covalent geometry : angle 0.72509 / 0.35 (32681) hydrogen bonds : bond 0.04849 / 3.25 ( 944) hydrogen bonds : angle 4.50204 / 3.20 ( 2857) metal coordination : bond 0.00389 / 0.29 ( 4) Misc. bond : bond 0.00048 / 0.03 ( 4) =============================================================================== Job complete usr+sys time: 11175.62 seconds wall clock time: 190 minutes 1.17 seconds (11401.17 seconds total)