Starting phenix.real_space_refine on Fri Jul 3 11:47:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1y_39740/07_2026/8z1y_39740_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1y_39740/07_2026/8z1y_39740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1y_39740/07_2026/8z1y_39740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1y_39740/07_2026/8z1y_39740.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1y_39740/07_2026/8z1y_39740_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1y_39740/07_2026/8z1y_39740_neut.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 6 5.49 5 S 97 5.16 5 C 8885 2.51 5 N 2385 2.21 5 O 2516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13897 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2562 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 17, 'TRANS': 313} Chain: "B" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2187 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 17, 'TRANS': 271} Chain: "C" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2486 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 20, 'TRANS': 303} Chain: "D" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2537 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 22, 'TRANS': 299} Chain: "F" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4047 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 31, 'TRANS': 475} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'AGS': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'AGS': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6915 SG CYS C 284 31.671 22.952 136.390 1.00119.16 S ATOM 6963 SG CYS C 290 36.378 24.091 141.226 1.00 99.77 S ATOM 7019 SG CYS C 297 32.458 18.954 141.089 1.00135.73 S ATOM 7155 SG CYS C 315 30.081 24.869 142.406 1.00101.76 S ATOM 9586 SG CYS D 306 48.994 78.583 135.298 1.00123.84 S ATOM 9715 SG CYS D 323 51.547 73.100 137.713 1.00119.19 S ATOM 9479 SG CYS D 293 49.392 73.791 131.595 1.00113.07 S ATOM 9525 SG CYS D 299 45.114 73.565 136.781 1.00120.68 S Time building chain proxies: 2.94, per 1000 atoms: 0.21 Number of scatterers: 13897 At special positions: 0 Unit cell: (84.24, 93.6, 161.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 97 16.00 P 6 15.00 O 2516 8.00 N 2385 7.00 C 8885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 34 " - pdb=" SG CYS F 262 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 644.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 402 " pdb="FE4 SF4 C 402 " - pdb=" SG CYS C 315 " pdb="FE2 SF4 C 402 " - pdb=" SG CYS C 290 " pdb="FE3 SF4 C 402 " - pdb=" SG CYS C 297 " pdb="FE1 SF4 C 402 " - pdb=" SG CYS C 284 " pdb=" SF4 D 401 " pdb="FE2 SF4 D 401 " - pdb=" SG CYS D 323 " pdb="FE3 SF4 D 401 " - pdb=" SG CYS D 293 " pdb="FE4 SF4 D 401 " - pdb=" SG CYS D 299 " pdb="FE1 SF4 D 401 " - pdb=" SG CYS D 306 " Number of angles added : 24 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 12 sheets defined 54.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 87 through 124 Proline residue: A 94 - end of helix Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 127 through 143 Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.648A pdb=" N ALA A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 205 through 232 removed outlier: 4.252A pdb=" N ILE A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.935A pdb=" N VAL A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 254 through 277 removed outlier: 3.987A pdb=" N ASN A 258 " --> pdb=" O HIS A 254 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.736A pdb=" N TRP A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.871A pdb=" N MET A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'B' and resid 17 through 28 removed outlier: 4.063A pdb=" N ARG B 28 " --> pdb=" O HIS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 48 removed outlier: 3.540A pdb=" N VAL B 33 " --> pdb=" O ASN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.528A pdb=" N ILE B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 4.191A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 127 removed outlier: 4.185A pdb=" N ARG B 99 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 144 removed outlier: 3.543A pdb=" N ASP B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 158 Processing helix chain 'B' and resid 160 through 188 removed outlier: 3.830A pdb=" N ALA B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Proline residue: B 174 - end of helix removed outlier: 3.742A pdb=" N VAL B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 3.501A pdb=" N THR B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'B' and resid 215 through 239 removed outlier: 4.177A pdb=" N LEU B 219 " --> pdb=" O CYS B 215 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 266 through 295 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 79 through 90 removed outlier: 4.012A pdb=" N ALA C 89 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 107 through 120 removed outlier: 4.057A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 148 through 149 No H-bonds generated for 'chain 'C' and resid 148 through 149' Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.549A pdb=" N CYS C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 204 Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'C' and resid 238 through 242 removed outlier: 4.243A pdb=" N PHE C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 242' Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 256 through 261 removed outlier: 6.039A pdb=" N GLU C 259 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 69 Processing helix chain 'D' and resid 90 through 100 removed outlier: 4.346A pdb=" N LYS D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.872A pdb=" N GLY D 110 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 Proline residue: D 125 - end of helix Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 163 through 177 Processing helix chain 'D' and resid 193 through 212 Processing helix chain 'D' and resid 221 through 229 removed outlier: 3.506A pdb=" N VAL D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 255 through 263 Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.922A pdb=" N THR D 307 " --> pdb=" O GLY D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.620A pdb=" N LEU F 46 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE F 47 " --> pdb=" O PRO F 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 43 through 47' Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.584A pdb=" N ALA F 55 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 127 removed outlier: 3.698A pdb=" N VAL F 118 " --> pdb=" O ASN F 114 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 Processing helix chain 'F' and resid 140 through 146 Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 173 through 178 Processing helix chain 'F' and resid 179 through 184 removed outlier: 6.697A pdb=" N PHE F 182 " --> pdb=" O ALA F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 201 through 206 Processing helix chain 'F' and resid 249 through 259 removed outlier: 3.501A pdb=" N TYR F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'F' and resid 272 through 278 removed outlier: 3.802A pdb=" N GLN F 278 " --> pdb=" O ALA F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 316 Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'F' and resid 355 through 366 Processing helix chain 'F' and resid 388 through 402 Processing helix chain 'F' and resid 413 through 423 Processing helix chain 'F' and resid 440 through 449 removed outlier: 4.224A pdb=" N THR F 446 " --> pdb=" O ASN F 442 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER F 449 " --> pdb=" O ALA F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 455 Processing helix chain 'F' and resid 464 through 472 removed outlier: 3.941A pdb=" N LEU F 470 " --> pdb=" O PRO F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 477 removed outlier: 3.535A pdb=" N ALA F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 498 Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 30 removed outlier: 6.565A pdb=" N ALA C 22 " --> pdb=" O HIS C 12 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N HIS C 12 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP C 24 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER C 10 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE C 26 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 30 removed outlier: 6.565A pdb=" N ALA C 22 " --> pdb=" O HIS C 12 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N HIS C 12 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP C 24 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER C 10 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE C 26 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.440A pdb=" N VAL C 35 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE C 225 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY C 37 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N MET C 227 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL C 39 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 224 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR C 235 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 226 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 33 through 39 removed outlier: 6.441A pdb=" N LYS D 20 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP D 39 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 18 " --> pdb=" O ASP D 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 39 removed outlier: 6.441A pdb=" N LYS D 20 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP D 39 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 18 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU D 18 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY D 76 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 101 through 104 removed outlier: 6.891A pdb=" N GLN D 102 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ASP D 186 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 104 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR D 50 " --> pdb=" O GLU D 231 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N MET D 233 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA D 52 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N MET D 235 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 54 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 242 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR D 236 " --> pdb=" O CYS D 240 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 30 through 33 removed outlier: 6.299A pdb=" N LYS F 227 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU F 215 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AA9, first strand: chain 'F' and resid 79 through 84 removed outlier: 3.692A pdb=" N LYS F 81 " --> pdb=" O HIS F 94 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR F 162 " --> pdb=" O LYS F 157 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS F 157 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN F 164 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL F 155 " --> pdb=" O GLN F 164 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL F 166 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 282 through 288 Processing sheet with id=AB2, first strand: chain 'F' and resid 282 through 288 removed outlier: 6.828A pdb=" N GLY F 293 " --> pdb=" O ILE F 503 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS F 505 " --> pdb=" O ASN F 291 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN F 291 " --> pdb=" O HIS F 505 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 516 through 517 719 hydrogen bonds defined for protein. 2061 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: 2.23 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 5973 1.42 - 1.64: 8064 1.64 - 1.86: 156 1.86 - 2.07: 1 2.07 - 2.29: 24 Bond restraints: 14218 Sorted by residual: bond pdb=" CE1 HIS B 24 " pdb=" NE2 HIS B 24 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.70e+01 bond pdb=" CD2 HIS B 24 " pdb=" NE2 HIS B 24 " ideal model delta sigma weight residual 1.374 1.285 0.089 1.10e-02 8.26e+03 6.55e+01 bond pdb=" CZ ARG D 273 " pdb=" NH2 ARG D 273 " ideal model delta sigma weight residual 1.330 1.229 0.101 1.30e-02 5.92e+03 6.04e+01 bond pdb=" CZ ARG D 274 " pdb=" NH2 ARG D 274 " ideal model delta sigma weight residual 1.330 1.229 0.101 1.30e-02 5.92e+03 5.99e+01 bond pdb=" CA ALA B 12 " pdb=" CB ALA B 12 " ideal model delta sigma weight residual 1.530 1.421 0.109 1.46e-02 4.69e+03 5.54e+01 ... (remaining 14213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 15766 2.52 - 5.04: 3268 5.04 - 7.55: 250 7.55 - 10.07: 39 10.07 - 12.59: 9 Bond angle restraints: 19332 Sorted by residual: angle pdb=" C GLU F 154 " pdb=" N VAL F 155 " pdb=" CA VAL F 155 " ideal model delta sigma weight residual 122.96 131.14 -8.18 9.50e-01 1.11e+00 7.42e+01 angle pdb=" N PRO B 246 " pdb=" CA PRO B 246 " pdb=" C PRO B 246 " ideal model delta sigma weight residual 110.70 120.53 -9.83 1.22e+00 6.72e-01 6.49e+01 angle pdb=" CA PHE F 443 " pdb=" CB PHE F 443 " pdb=" CG PHE F 443 " ideal model delta sigma weight residual 113.80 120.88 -7.08 1.00e+00 1.00e+00 5.01e+01 angle pdb=" CA ASP C 321 " pdb=" CB ASP C 321 " pdb=" CG ASP C 321 " ideal model delta sigma weight residual 112.60 119.52 -6.92 1.00e+00 1.00e+00 4.80e+01 angle pdb=" CA ASP D 85 " pdb=" CB ASP D 85 " pdb=" CG ASP D 85 " ideal model delta sigma weight residual 112.60 119.36 -6.76 1.00e+00 1.00e+00 4.57e+01 ... (remaining 19327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.81: 8293 26.81 - 53.62: 265 53.62 - 80.42: 44 80.42 - 107.23: 7 107.23 - 134.04: 2 Dihedral angle restraints: 8611 sinusoidal: 3508 harmonic: 5103 Sorted by residual: dihedral pdb=" CB CYS F 34 " pdb=" SG CYS F 34 " pdb=" SG CYS F 262 " pdb=" CB CYS F 262 " ideal model delta sinusoidal sigma weight residual 93.00 -176.58 -90.42 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" C ILE A 215 " pdb=" N ILE A 215 " pdb=" CA ILE A 215 " pdb=" CB ILE A 215 " ideal model delta harmonic sigma weight residual -122.00 -136.89 14.89 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA ALA F 500 " pdb=" C ALA F 500 " pdb=" N LEU F 501 " pdb=" CA LEU F 501 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1878 0.161 - 0.321: 196 0.321 - 0.482: 42 0.482 - 0.642: 48 0.642 - 0.802: 13 Chirality restraints: 2177 Sorted by residual: chirality pdb=" CG LEU A 6 " pdb=" CB LEU A 6 " pdb=" CD1 LEU A 6 " pdb=" CD2 LEU A 6 " both_signs ideal model delta sigma weight residual False -2.59 -1.79 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CB VAL B 14 " pdb=" CA VAL B 14 " pdb=" CG1 VAL B 14 " pdb=" CG2 VAL B 14 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CB VAL B 137 " pdb=" CA VAL B 137 " pdb=" CG1 VAL B 137 " pdb=" CG2 VAL B 137 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 2174 not shown) Planarity restraints: 2477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AGS C 401 " -0.252 2.00e-02 2.50e+03 1.03e-01 2.94e+02 pdb=" C2 AGS C 401 " 0.031 2.00e-02 2.50e+03 pdb=" C4 AGS C 401 " 0.097 2.00e-02 2.50e+03 pdb=" C5 AGS C 401 " 0.053 2.00e-02 2.50e+03 pdb=" C6 AGS C 401 " -0.035 2.00e-02 2.50e+03 pdb=" C8 AGS C 401 " 0.049 2.00e-02 2.50e+03 pdb=" N1 AGS C 401 " -0.048 2.00e-02 2.50e+03 pdb=" N3 AGS C 401 " 0.086 2.00e-02 2.50e+03 pdb=" N6 AGS C 401 " -0.126 2.00e-02 2.50e+03 pdb=" N7 AGS C 401 " 0.055 2.00e-02 2.50e+03 pdb=" N9 AGS C 401 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 132 " 0.189 2.00e-02 2.50e+03 1.10e-01 2.42e+02 pdb=" CG TYR F 132 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 132 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR F 132 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 TYR F 132 " -0.076 2.00e-02 2.50e+03 pdb=" CE2 TYR F 132 " -0.077 2.00e-02 2.50e+03 pdb=" CZ TYR F 132 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR F 132 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 96 " -0.154 2.00e-02 2.50e+03 8.25e-02 1.36e+02 pdb=" CG TYR B 96 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 96 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR B 96 " 0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR B 96 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR B 96 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR B 96 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 96 " -0.124 2.00e-02 2.50e+03 ... (remaining 2474 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4030 2.87 - 3.37: 13449 3.37 - 3.88: 23754 3.88 - 4.39: 27401 4.39 - 4.90: 47184 Nonbonded interactions: 115818 Sorted by model distance: nonbonded pdb=" O ALA F 445 " pdb=" OG SER F 449 " model vdw 2.358 3.040 nonbonded pdb=" OG1 THR B 17 " pdb=" OE1 GLN B 20 " model vdw 2.451 3.040 nonbonded pdb=" OD1 ASP D 271 " pdb=" N ASP D 272 " model vdw 2.452 3.120 nonbonded pdb=" N CYS F 450 " pdb=" OE2 GLU F 468 " model vdw 2.508 3.120 nonbonded pdb=" OD1 ASP F 249 " pdb=" OG SER F 251 " model vdw 2.541 3.040 ... (remaining 115813 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.720 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.016 0.156 14227 Z= 0.921 Angle : 1.981 17.876 19358 Z= 1.312 Chirality : 0.146 0.802 2177 Planarity : 0.016 0.123 2477 Dihedral : 13.779 134.041 5332 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % Favored : 99.26 % Cbeta Deviations : 2.20 % 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: -1.30 (0.18), residues: 1763 helix: -1.25 (0.15), residues: 855 sheet: -0.69 (0.40), residues: 162 loop : -0.13 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG C 62 TYR 0.189 0.022 TYR F 132 PHE 0.097 0.015 PHE A 24 TRP 0.088 0.024 TRP F 433 HIS 0.016 0.004 HIS C 212 Details of bonding type rmsd/Z covalent geometry : bond 0.01605 / 0.92 (14218) covalent geometry : angle 1.96489 / 1.31 (19332) SS BOND : bond 0.01324 / 0.70 ( 1) SS BOND : angle 3.72086 / 2.11 ( 2) hydrogen bonds : bond 0.17024 / 11.51 ( 703) hydrogen bonds : angle 7.80604 / 5.78 ( 2061) metal coordination : bond 0.09776 / 4.74 ( 8) metal coordination : angle 7.44358 / 5.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7285 (tpp) cc_final: 0.7000 (tpt) REVERT: A 151 MET cc_start: 0.6573 (mtp) cc_final: 0.6263 (mtp) REVERT: A 197 ASN cc_start: 0.7801 (t0) cc_final: 0.7198 (m-40) REVERT: A 200 ASP cc_start: 0.6644 (t70) cc_final: 0.6166 (t0) REVERT: A 205 MET cc_start: 0.7374 (tpp) cc_final: 0.6902 (mmm) REVERT: A 223 MET cc_start: 0.7614 (tpp) cc_final: 0.7317 (tpt) REVERT: A 228 MET cc_start: 0.6819 (mmm) cc_final: 0.6574 (mmt) REVERT: A 246 THR cc_start: 0.7366 (t) cc_final: 0.7132 (p) REVERT: A 247 ARG cc_start: 0.6668 (mmm160) cc_final: 0.6301 (mmm160) REVERT: A 248 MET cc_start: 0.6831 (mmt) cc_final: 0.6566 (mmm) REVERT: A 273 THR cc_start: 0.7302 (m) cc_final: 0.6890 (p) REVERT: A 325 ASP cc_start: 0.6989 (t70) cc_final: 0.6718 (t0) REVERT: B 77 MET cc_start: 0.6988 (tpt) cc_final: 0.6565 (tpt) REVERT: B 141 MET cc_start: 0.7220 (mtt) cc_final: 0.6974 (mtp) REVERT: B 205 ARG cc_start: 0.7186 (ttm-80) cc_final: 0.6778 (ttt-90) REVERT: B 207 MET cc_start: 0.7495 (ptt) cc_final: 0.7280 (ptt) REVERT: B 224 SER cc_start: 0.7726 (m) cc_final: 0.7176 (p) REVERT: B 254 MET cc_start: 0.7660 (ptm) cc_final: 0.7401 (ptp) REVERT: C 24 ASP cc_start: 0.7924 (t0) cc_final: 0.7641 (t0) REVERT: C 26 ILE cc_start: 0.7092 (mm) cc_final: 0.6857 (mm) REVERT: C 32 GLN cc_start: 0.7315 (mp10) cc_final: 0.7023 (mp10) REVERT: C 46 LYS cc_start: 0.6380 (mtmt) cc_final: 0.6083 (mtpt) REVERT: C 53 ILE cc_start: 0.7933 (pt) cc_final: 0.7589 (mp) REVERT: C 67 LYS cc_start: 0.7425 (mtmm) cc_final: 0.6841 (mtmm) REVERT: C 73 GLN cc_start: 0.6530 (mp-120) cc_final: 0.6142 (mp-120) REVERT: C 90 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6885 (mt-10) REVERT: C 97 ASP cc_start: 0.6894 (t0) cc_final: 0.6678 (t0) REVERT: C 106 TYR cc_start: 0.8126 (m-80) cc_final: 0.7653 (m-80) REVERT: C 117 LYS cc_start: 0.7284 (ttpt) cc_final: 0.6961 (ttpt) REVERT: C 120 GLN cc_start: 0.7986 (mt0) cc_final: 0.7785 (mt0) REVERT: C 173 LYS cc_start: 0.7228 (mtpt) cc_final: 0.6855 (mtpp) REVERT: C 203 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7032 (mt-10) REVERT: C 205 MET cc_start: 0.8007 (ptt) cc_final: 0.7720 (ptp) REVERT: C 219 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7067 (mt-10) REVERT: C 251 GLN cc_start: 0.7566 (tt0) cc_final: 0.7280 (tt0) REVERT: C 255 ARG cc_start: 0.7373 (mtt180) cc_final: 0.7094 (mtt180) REVERT: C 266 ARG cc_start: 0.7306 (mpt180) cc_final: 0.7089 (mmt-90) REVERT: D 25 LYS cc_start: 0.7645 (mtpt) cc_final: 0.6981 (mtpm) REVERT: D 36 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7381 (tppp) REVERT: D 39 ASP cc_start: 0.7065 (m-30) cc_final: 0.6804 (m-30) REVERT: D 47 ARG cc_start: 0.6962 (ptm160) cc_final: 0.6759 (ptm160) REVERT: D 56 GLU cc_start: 0.6895 (tp30) cc_final: 0.6521 (tp30) REVERT: D 73 MET cc_start: 0.7775 (mmt) cc_final: 0.7428 (mmt) REVERT: D 78 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7215 (mt-10) REVERT: D 100 LYS cc_start: 0.7152 (mmtt) cc_final: 0.6933 (mmtm) REVERT: D 147 LYS cc_start: 0.7479 (mtpt) cc_final: 0.7263 (mtmm) REVERT: D 161 MET cc_start: 0.7826 (ptp) cc_final: 0.7621 (ptp) REVERT: D 176 LEU cc_start: 0.8258 (mt) cc_final: 0.8037 (mm) REVERT: D 206 ASP cc_start: 0.6679 (m-30) cc_final: 0.6455 (m-30) REVERT: D 208 GLN cc_start: 0.6993 (tt0) cc_final: 0.6690 (tt0) REVERT: D 209 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7469 (mm-40) REVERT: D 226 GLU cc_start: 0.7735 (tt0) cc_final: 0.7401 (tt0) REVERT: D 231 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7364 (mt-10) REVERT: D 242 GLU cc_start: 0.8203 (tt0) cc_final: 0.7955 (tt0) REVERT: D 243 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7393 (ttpp) REVERT: D 247 ASP cc_start: 0.6827 (p0) cc_final: 0.6584 (p0) REVERT: D 251 ASN cc_start: 0.7893 (m110) cc_final: 0.7500 (m-40) REVERT: D 300 ARG cc_start: 0.7580 (ptt-90) cc_final: 0.7232 (ptt-90) REVERT: D 312 GLN cc_start: 0.7344 (mt0) cc_final: 0.6946 (mt0) REVERT: F 66 GLU cc_start: 0.7425 (pt0) cc_final: 0.7191 (pt0) REVERT: F 73 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6356 (tt0) REVERT: F 97 LYS cc_start: 0.7985 (mptt) cc_final: 0.7412 (mmtm) REVERT: F 100 LYS cc_start: 0.7741 (ptpt) cc_final: 0.6839 (ptpp) REVERT: F 146 MET cc_start: 0.7657 (mmm) cc_final: 0.6869 (mmm) REVERT: F 156 LYS cc_start: 0.7643 (mtmm) cc_final: 0.7352 (mtpp) REVERT: F 169 ARG cc_start: 0.7012 (ptt-90) cc_final: 0.6617 (ptt90) REVERT: F 180 MET cc_start: 0.7437 (mtp) cc_final: 0.7045 (mtm) REVERT: F 195 MET cc_start: 0.7249 (tpt) cc_final: 0.6763 (tpt) REVERT: F 201 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6250 (mm-30) REVERT: F 273 ILE cc_start: 0.6760 (mt) cc_final: 0.6423 (mm) REVERT: F 280 LYS cc_start: 0.7747 (mmtm) cc_final: 0.7472 (mmmm) REVERT: F 286 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7147 (mt-10) REVERT: F 306 ASP cc_start: 0.6438 (t0) cc_final: 0.6229 (m-30) REVERT: F 328 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7666 (mp10) REVERT: F 342 MET cc_start: 0.8102 (ttm) cc_final: 0.7863 (ttp) REVERT: F 357 GLU cc_start: 0.6278 (mp0) cc_final: 0.6039 (mp0) REVERT: F 364 LYS cc_start: 0.7649 (ttpp) cc_final: 0.7327 (tttp) REVERT: F 395 MET cc_start: 0.7147 (mtm) cc_final: 0.6917 (mtp) REVERT: F 406 GLN cc_start: 0.7798 (mt0) cc_final: 0.7491 (mt0) REVERT: F 416 GLU cc_start: 0.7033 (tt0) cc_final: 0.6454 (tp30) REVERT: F 419 LYS cc_start: 0.7174 (tttp) cc_final: 0.6726 (ttpp) REVERT: F 420 ARG cc_start: 0.7258 (mtt-85) cc_final: 0.6863 (mtp85) REVERT: F 423 ASP cc_start: 0.7133 (t0) cc_final: 0.6700 (t0) REVERT: F 430 MET cc_start: 0.7605 (tpp) cc_final: 0.7182 (mmm) REVERT: F 449 SER cc_start: 0.7491 (p) cc_final: 0.7030 (m) REVERT: F 461 LYS cc_start: 0.7343 (mmtt) cc_final: 0.7063 (mptt) REVERT: F 485 GLU cc_start: 0.6828 (tt0) cc_final: 0.6608 (tt0) REVERT: F 489 GLN cc_start: 0.6763 (mm-40) cc_final: 0.6505 (mm-40) REVERT: F 515 GLU cc_start: 0.7196 (tt0) cc_final: 0.6983 (tt0) REVERT: F 530 GLU cc_start: 0.7523 (pm20) cc_final: 0.7245 (pm20) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.5909 time to fit residues: 291.2465 Evaluate side-chains 401 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0970 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 299 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 210 ASN C 96 GLN C 191 GLN C 201 GLN C 231 GLN D 120 GLN D 251 ASN F 43 ASN F 455 GLN F 527 HIS F 531 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118428 restraints weight = 17584.359| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.44 r_work: 0.3508 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14227 Z= 0.145 Angle : 0.667 14.944 19358 Z= 0.334 Chirality : 0.046 0.236 2177 Planarity : 0.005 0.049 2477 Dihedral : 9.139 152.254 1996 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.82 % Allowed : 10.72 % Favored : 87.46 % 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: 0.25 (0.20), residues: 1763 helix: 0.43 (0.17), residues: 869 sheet: -0.48 (0.38), residues: 170 loop : 0.23 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 298 TYR 0.019 0.002 TYR B 25 PHE 0.023 0.002 PHE F 107 TRP 0.022 0.002 TRP A 293 HIS 0.006 0.001 HIS C 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (14218) covalent geometry : angle 0.63165 / 0.33 (19332) SS BOND : bond 0.00146 / 0.08 ( 1) SS BOND : angle 2.73411 / 1.60 ( 2) hydrogen bonds : bond 0.04543 / 3.08 ( 703) hydrogen bonds : angle 5.43887 / 4.03 ( 2061) metal coordination : bond 0.01119 / 0.55 ( 8) metal coordination : angle 6.04107 / 4.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 379 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7988 (mt) REVERT: A 56 LEU cc_start: 0.8282 (mt) cc_final: 0.8027 (mp) REVERT: A 205 MET cc_start: 0.8061 (tpp) cc_final: 0.7829 (mmm) REVERT: A 223 MET cc_start: 0.8324 (tpp) cc_final: 0.7967 (tpt) REVERT: B 205 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7568 (ttt90) REVERT: C 13 PHE cc_start: 0.7997 (m-80) cc_final: 0.7670 (m-80) REVERT: C 34 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: C 44 SER cc_start: 0.7612 (m) cc_final: 0.7384 (p) REVERT: C 73 GLN cc_start: 0.7807 (mp-120) cc_final: 0.7440 (mp-120) REVERT: C 117 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7688 (ttpt) REVERT: C 137 GLN cc_start: 0.7963 (mt0) cc_final: 0.7735 (mt0) REVERT: C 179 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: C 189 GLN cc_start: 0.8328 (tt0) cc_final: 0.8072 (tt0) REVERT: C 203 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7450 (mt-10) REVERT: C 227 MET cc_start: 0.8141 (ttm) cc_final: 0.7925 (mtt) REVERT: D 49 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8340 (mttp) REVERT: D 195 SER cc_start: 0.7903 (t) cc_final: 0.7665 (m) REVERT: D 226 GLU cc_start: 0.7784 (tt0) cc_final: 0.7579 (tt0) REVERT: D 312 GLN cc_start: 0.7732 (mt0) cc_final: 0.7503 (mt0) REVERT: F 54 ASP cc_start: 0.7602 (m-30) cc_final: 0.7389 (m-30) REVERT: F 106 GLU cc_start: 0.6838 (pt0) cc_final: 0.6559 (pt0) REVERT: F 129 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7588 (mp-120) REVERT: F 146 MET cc_start: 0.7905 (mmm) cc_final: 0.7545 (mmm) REVERT: F 180 MET cc_start: 0.8091 (mtp) cc_final: 0.7889 (mtm) REVERT: F 342 MET cc_start: 0.8448 (ttm) cc_final: 0.8150 (ttp) REVERT: F 357 GLU cc_start: 0.7065 (mp0) cc_final: 0.6816 (mp0) outliers start: 27 outliers final: 11 residues processed: 382 average time/residue: 0.6234 time to fit residues: 258.3969 Evaluate side-chains 361 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 346 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 287 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 108 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 164 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN B 20 GLN B 60 GLN B 210 ASN C 96 GLN C 120 GLN C 189 GLN C 191 GLN D 21 HIS D 129 ASN D 208 GLN F 206 ASN F 472 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.124370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.114724 restraints weight = 17978.672| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.53 r_work: 0.3460 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14227 Z= 0.250 Angle : 0.706 19.003 19358 Z= 0.341 Chirality : 0.049 0.247 2177 Planarity : 0.005 0.063 2477 Dihedral : 8.551 155.726 1996 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.97 % Allowed : 14.57 % Favored : 82.47 % 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 (0.20), residues: 1763 helix: 0.44 (0.17), residues: 872 sheet: -0.78 (0.36), residues: 188 loop : 0.19 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 47 TYR 0.021 0.003 TYR F 412 PHE 0.021 0.002 PHE F 107 TRP 0.019 0.002 TRP A 293 HIS 0.007 0.002 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.25 (14218) covalent geometry : angle 0.66254 / 0.34 (19332) SS BOND : bond 0.00563 / 0.30 ( 1) SS BOND : angle 2.08854 / 1.23 ( 2) hydrogen bonds : bond 0.04633 / 3.14 ( 703) hydrogen bonds : angle 5.26029 / 3.92 ( 2061) metal coordination : bond 0.01516 / 0.71 ( 8) metal coordination : angle 6.92756 / 4.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 379 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8266 (mt) cc_final: 0.7932 (mt) REVERT: A 56 LEU cc_start: 0.8301 (mt) cc_final: 0.8053 (mp) REVERT: A 205 MET cc_start: 0.8079 (tpp) cc_final: 0.7870 (mmm) REVERT: A 223 MET cc_start: 0.8326 (tpp) cc_final: 0.8054 (tpt) REVERT: A 247 ARG cc_start: 0.7451 (mmm160) cc_final: 0.7219 (mmm160) REVERT: B 22 PHE cc_start: 0.7899 (t80) cc_final: 0.7640 (t80) REVERT: B 62 ARG cc_start: 0.8450 (mmt90) cc_final: 0.7996 (mpt180) REVERT: B 205 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7534 (ttt90) REVERT: B 228 SER cc_start: 0.7930 (t) cc_final: 0.7653 (p) REVERT: C 101 SER cc_start: 0.7844 (t) cc_final: 0.7622 (p) REVERT: C 117 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7767 (ttpt) REVERT: C 158 MET cc_start: 0.8414 (mtp) cc_final: 0.8187 (mtm) REVERT: C 203 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7470 (mt-10) REVERT: C 227 MET cc_start: 0.8396 (ttm) cc_final: 0.8164 (mtt) REVERT: C 255 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7651 (ttm110) REVERT: D 195 SER cc_start: 0.7984 (t) cc_final: 0.7691 (m) REVERT: D 249 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7846 (mt) REVERT: D 300 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7401 (ptt-90) REVERT: D 312 GLN cc_start: 0.7855 (mt0) cc_final: 0.7618 (mt0) REVERT: F 54 ASP cc_start: 0.7706 (m-30) cc_final: 0.7477 (m-30) REVERT: F 86 GLU cc_start: 0.7710 (mp0) cc_final: 0.7396 (mp0) REVERT: F 129 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7734 (mp-120) REVERT: F 202 LYS cc_start: 0.7735 (mttt) cc_final: 0.7489 (mtpt) REVERT: F 357 GLU cc_start: 0.7109 (mp0) cc_final: 0.6838 (mp0) REVERT: F 449 SER cc_start: 0.7670 (t) cc_final: 0.7379 (m) REVERT: F 475 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8153 (ttm170) REVERT: F 496 ASP cc_start: 0.7949 (t0) cc_final: 0.7747 (t70) outliers start: 44 outliers final: 18 residues processed: 385 average time/residue: 0.6107 time to fit residues: 256.2326 Evaluate side-chains 380 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 360 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 300 ARG Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 338 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 64 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 141 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN B 79 HIS B 210 ASN C 120 GLN C 179 GLN C 212 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115001 restraints weight = 17895.699| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.44 r_work: 0.3476 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14227 Z= 0.221 Angle : 0.675 19.267 19358 Z= 0.324 Chirality : 0.047 0.257 2177 Planarity : 0.005 0.053 2477 Dihedral : 7.953 166.945 1996 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.84 % Allowed : 16.25 % Favored : 79.91 % 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: 0.22 (0.20), residues: 1763 helix: 0.55 (0.17), residues: 867 sheet: -0.79 (0.36), residues: 184 loop : 0.12 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 298 TYR 0.020 0.002 TYR F 140 PHE 0.019 0.002 PHE F 107 TRP 0.017 0.002 TRP A 293 HIS 0.006 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (14218) covalent geometry : angle 0.63186 / 0.32 (19332) SS BOND : bond 0.00410 / 0.22 ( 1) SS BOND : angle 1.96412 / 1.15 ( 2) hydrogen bonds : bond 0.04296 / 2.93 ( 703) hydrogen bonds : angle 5.16061 / 3.86 ( 2061) metal coordination : bond 0.01206 / 0.54 ( 8) metal coordination : angle 6.77119 / 3.83 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 380 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8311 (mt) cc_final: 0.7950 (mt) REVERT: A 56 LEU cc_start: 0.8327 (mt) cc_final: 0.8077 (mp) REVERT: A 223 MET cc_start: 0.8328 (tpp) cc_final: 0.8095 (tpt) REVERT: B 62 ARG cc_start: 0.8451 (mmt90) cc_final: 0.8103 (mpt180) REVERT: B 205 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7509 (ttt90) REVERT: B 228 SER cc_start: 0.7935 (t) cc_final: 0.7683 (p) REVERT: C 16 GLU cc_start: 0.7756 (tp30) cc_final: 0.7551 (tp30) REVERT: C 101 SER cc_start: 0.7790 (t) cc_final: 0.7580 (p) REVERT: C 117 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7716 (ttpt) REVERT: C 129 GLN cc_start: 0.7941 (tp40) cc_final: 0.7718 (tp-100) REVERT: C 203 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7441 (mt-10) REVERT: C 227 MET cc_start: 0.8401 (ttm) cc_final: 0.8170 (mtt) REVERT: C 241 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8147 (tt) REVERT: C 265 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6670 (mm-30) REVERT: D 195 SER cc_start: 0.8002 (t) cc_final: 0.7788 (m) REVERT: D 249 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7872 (mt) REVERT: D 300 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7352 (ptt-90) REVERT: D 312 GLN cc_start: 0.7855 (mt0) cc_final: 0.7624 (mt0) REVERT: F 54 ASP cc_start: 0.7691 (m-30) cc_final: 0.7487 (m-30) REVERT: F 86 GLU cc_start: 0.7608 (mp0) cc_final: 0.7284 (mp0) REVERT: F 129 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7674 (mp-120) REVERT: F 357 GLU cc_start: 0.7091 (mp0) cc_final: 0.6857 (mp0) REVERT: F 430 MET cc_start: 0.8080 (mmm) cc_final: 0.7843 (mmm) REVERT: F 449 SER cc_start: 0.7617 (t) cc_final: 0.7355 (m) REVERT: F 475 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8173 (ttm170) outliers start: 57 outliers final: 23 residues processed: 393 average time/residue: 0.6654 time to fit residues: 284.1493 Evaluate side-chains 391 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 365 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 300 ARG Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 338 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 152 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 162 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN B 210 ASN B 214 ASN C 120 GLN C 179 GLN C 212 HIS F 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.123617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114248 restraints weight = 18067.088| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.47 r_work: 0.3468 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14227 Z= 0.231 Angle : 0.674 19.510 19358 Z= 0.323 Chirality : 0.047 0.269 2177 Planarity : 0.005 0.052 2477 Dihedral : 7.711 176.435 1996 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.51 % Allowed : 17.67 % Favored : 78.83 % 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: 0.20 (0.20), residues: 1763 helix: 0.56 (0.17), residues: 866 sheet: -0.78 (0.36), residues: 184 loop : 0.06 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 420 TYR 0.022 0.002 TYR F 140 PHE 0.031 0.002 PHE F 107 TRP 0.014 0.002 TRP A 293 HIS 0.007 0.001 HIS C 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (14218) covalent geometry : angle 0.63068 / 0.32 (19332) SS BOND : bond 0.00502 / 0.26 ( 1) SS BOND : angle 1.78114 / 1.05 ( 2) hydrogen bonds : bond 0.04276 / 2.92 ( 703) hydrogen bonds : angle 5.14929 / 3.86 ( 2061) metal coordination : bond 0.01326 / 0.60 ( 8) metal coordination : angle 6.76398 / 3.72 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 383 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8338 (mt) cc_final: 0.8101 (mp) REVERT: A 223 MET cc_start: 0.8342 (tpp) cc_final: 0.8021 (tpt) REVERT: B 62 ARG cc_start: 0.8436 (mmt90) cc_final: 0.8016 (mpt180) REVERT: B 205 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7507 (ttt90) REVERT: B 207 MET cc_start: 0.8504 (ptt) cc_final: 0.8267 (mtm) REVERT: B 228 SER cc_start: 0.7950 (t) cc_final: 0.7695 (p) REVERT: C 101 SER cc_start: 0.7797 (t) cc_final: 0.7567 (p) REVERT: C 117 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7740 (ttpt) REVERT: C 203 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7446 (mt-10) REVERT: C 227 MET cc_start: 0.8420 (ttm) cc_final: 0.8188 (mtt) REVERT: C 241 ILE cc_start: 0.8390 (mm) cc_final: 0.8127 (tt) REVERT: C 265 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6701 (mm-30) REVERT: D 33 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7522 (mtp85) REVERT: D 115 ARG cc_start: 0.8445 (mmt-90) cc_final: 0.8214 (mpt180) REVERT: D 195 SER cc_start: 0.7959 (t) cc_final: 0.7752 (m) REVERT: D 249 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7888 (mt) REVERT: D 300 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7326 (ptt-90) REVERT: D 312 GLN cc_start: 0.7839 (mt0) cc_final: 0.7610 (mt0) REVERT: F 42 PHE cc_start: 0.8593 (m-80) cc_final: 0.8002 (m-80) REVERT: F 54 ASP cc_start: 0.7689 (m-30) cc_final: 0.7478 (m-30) REVERT: F 86 GLU cc_start: 0.7540 (mp0) cc_final: 0.7212 (mp0) REVERT: F 129 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7753 (mp-120) REVERT: F 357 GLU cc_start: 0.7093 (mp0) cc_final: 0.6848 (mp0) REVERT: F 388 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8181 (t160) REVERT: F 449 SER cc_start: 0.7600 (t) cc_final: 0.7357 (m) outliers start: 52 outliers final: 29 residues processed: 397 average time/residue: 0.6469 time to fit residues: 278.8700 Evaluate side-chains 407 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 375 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 300 ARG Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 419 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 0.0040 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN B 210 ASN C 120 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.124903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115700 restraints weight = 17754.643| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.43 r_work: 0.3476 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14227 Z= 0.187 Angle : 0.643 18.686 19358 Z= 0.308 Chirality : 0.046 0.268 2177 Planarity : 0.005 0.049 2477 Dihedral : 7.434 178.363 1996 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.37 % Allowed : 18.61 % Favored : 78.02 % 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: 0.39 (0.20), residues: 1763 helix: 0.74 (0.17), residues: 864 sheet: -0.69 (0.37), residues: 184 loop : 0.12 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 28 TYR 0.019 0.002 TYR C 317 PHE 0.033 0.002 PHE F 107 TRP 0.015 0.001 TRP A 293 HIS 0.005 0.001 HIS C 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (14218) covalent geometry : angle 0.59989 / 0.31 (19332) SS BOND : bond 0.00340 / 0.18 ( 1) SS BOND : angle 1.63949 / 0.96 ( 2) hydrogen bonds : bond 0.04046 / 2.78 ( 703) hydrogen bonds : angle 5.09488 / 3.81 ( 2061) metal coordination : bond 0.01063 / 0.47 ( 8) metal coordination : angle 6.58650 / 3.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 384 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8322 (mt) cc_final: 0.8092 (mp) REVERT: A 223 MET cc_start: 0.8372 (tpp) cc_final: 0.8045 (tpt) REVERT: A 271 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7896 (p) REVERT: B 62 ARG cc_start: 0.8455 (mmt90) cc_final: 0.8026 (mpt180) REVERT: B 205 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7473 (ttt90) REVERT: B 207 MET cc_start: 0.8453 (ptt) cc_final: 0.8238 (mtm) REVERT: B 228 SER cc_start: 0.7911 (t) cc_final: 0.7668 (p) REVERT: C 117 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7671 (ttpt) REVERT: C 203 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7399 (mt-10) REVERT: C 227 MET cc_start: 0.8417 (ttm) cc_final: 0.8203 (mtt) REVERT: C 241 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8070 (tt) REVERT: C 265 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6676 (mm-30) REVERT: D 25 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7872 (mtpm) REVERT: D 33 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7518 (mtp85) REVERT: D 115 ARG cc_start: 0.8428 (mmt-90) cc_final: 0.8185 (mpt180) REVERT: D 249 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7868 (mt) REVERT: F 42 PHE cc_start: 0.8584 (m-80) cc_final: 0.8094 (m-80) REVERT: F 86 GLU cc_start: 0.7549 (mp0) cc_final: 0.7219 (mp0) REVERT: F 129 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7735 (mp-120) REVERT: F 357 GLU cc_start: 0.7090 (mp0) cc_final: 0.6854 (mp0) REVERT: F 388 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8181 (t160) REVERT: F 449 SER cc_start: 0.7560 (t) cc_final: 0.7317 (m) REVERT: F 475 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8166 (ttm170) outliers start: 50 outliers final: 23 residues processed: 399 average time/residue: 0.6430 time to fit residues: 279.3867 Evaluate side-chains 403 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 375 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 298 ARG Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 419 LYS Chi-restraints excluded: chain F residue 425 GLU Chi-restraints excluded: chain F residue 501 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 129 optimal weight: 0.0070 chunk 32 optimal weight: 0.2980 chunk 44 optimal weight: 0.0670 chunk 6 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 147 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN B 60 GLN B 210 ASN C 120 GLN C 179 GLN C 200 GLN C 201 GLN C 212 HIS F 114 ASN F 298 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117732 restraints weight = 17717.240| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.43 r_work: 0.3505 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14227 Z= 0.121 Angle : 0.608 15.645 19358 Z= 0.291 Chirality : 0.043 0.273 2177 Planarity : 0.005 0.049 2477 Dihedral : 6.935 171.725 1996 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.56 % Allowed : 20.77 % Favored : 76.67 % 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: 0.68 (0.20), residues: 1763 helix: 1.00 (0.18), residues: 859 sheet: -0.57 (0.39), residues: 180 loop : 0.23 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 28 TYR 0.018 0.002 TYR F 140 PHE 0.034 0.001 PHE F 107 TRP 0.017 0.001 TRP A 293 HIS 0.004 0.001 HIS C 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (14218) covalent geometry : angle 0.56865 / 0.29 (19332) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 1.44016 / 0.85 ( 2) hydrogen bonds : bond 0.03600 / 2.47 ( 703) hydrogen bonds : angle 4.94419 / 3.69 ( 2061) metal coordination : bond 0.00708 / 0.28 ( 8) metal coordination : angle 6.12920 / 3.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 379 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8398 (tpp) cc_final: 0.8082 (tpt) REVERT: B 62 ARG cc_start: 0.8426 (mmt90) cc_final: 0.7964 (mpt180) REVERT: B 228 SER cc_start: 0.7829 (t) cc_final: 0.7594 (p) REVERT: C 117 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7613 (ttpt) REVERT: C 203 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7386 (mt-10) REVERT: C 241 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7922 (tt) REVERT: C 265 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6664 (mm-30) REVERT: D 33 ARG cc_start: 0.7691 (ttp80) cc_final: 0.7478 (mtp85) REVERT: D 176 LEU cc_start: 0.8906 (mt) cc_final: 0.8688 (mt) REVERT: D 249 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7836 (mt) REVERT: D 300 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7292 (ptt-90) REVERT: D 312 GLN cc_start: 0.7797 (mt0) cc_final: 0.7566 (mm-40) REVERT: F 42 PHE cc_start: 0.8547 (m-80) cc_final: 0.8021 (m-80) REVERT: F 86 GLU cc_start: 0.7494 (mp0) cc_final: 0.7157 (mp0) REVERT: F 129 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7742 (mp-120) REVERT: F 180 MET cc_start: 0.8070 (mtp) cc_final: 0.7822 (mtm) REVERT: F 241 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7712 (m) REVERT: F 449 SER cc_start: 0.7487 (t) cc_final: 0.7272 (m) REVERT: F 475 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8161 (ttm170) outliers start: 38 outliers final: 18 residues processed: 392 average time/residue: 0.6462 time to fit residues: 275.2669 Evaluate side-chains 388 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 366 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 300 ARG Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 425 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.2980 chunk 55 optimal weight: 0.0050 chunk 88 optimal weight: 0.2980 chunk 132 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 124 optimal weight: 0.0980 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 210 ASN C 120 GLN C 200 GLN F 388 ASN F 531 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117715 restraints weight = 17497.922| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.51 r_work: 0.3500 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14227 Z= 0.118 Angle : 0.598 14.488 19358 Z= 0.287 Chirality : 0.043 0.262 2177 Planarity : 0.005 0.065 2477 Dihedral : 6.778 170.569 1996 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.96 % Allowed : 21.98 % Favored : 76.06 % 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: 0.79 (0.20), residues: 1763 helix: 1.09 (0.18), residues: 861 sheet: -0.55 (0.38), residues: 190 loop : 0.32 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 255 TYR 0.016 0.002 TYR F 140 PHE 0.035 0.001 PHE F 107 TRP 0.018 0.001 TRP A 293 HIS 0.004 0.001 HIS F 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14218) covalent geometry : angle 0.56182 / 0.29 (19332) SS BOND : bond 0.00132 / 0.07 ( 1) SS BOND : angle 1.34130 / 0.79 ( 2) hydrogen bonds : bond 0.03525 / 2.41 ( 703) hydrogen bonds : angle 4.88377 / 3.65 ( 2061) metal coordination : bond 0.00626 / 0.26 ( 8) metal coordination : angle 5.87366 / 3.14 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 377 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8511 (tpt) cc_final: 0.8195 (tpt) REVERT: A 223 MET cc_start: 0.8387 (tpp) cc_final: 0.8086 (tpt) REVERT: B 62 ARG cc_start: 0.8404 (mmt90) cc_final: 0.7949 (mpt180) REVERT: B 228 SER cc_start: 0.7840 (t) cc_final: 0.7584 (p) REVERT: C 117 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7619 (ttpt) REVERT: C 203 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7396 (mt-10) REVERT: C 241 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7891 (tt) REVERT: C 265 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6643 (mm-30) REVERT: D 33 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7496 (mtp85) REVERT: D 176 LEU cc_start: 0.8874 (mt) cc_final: 0.8645 (mt) REVERT: D 249 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7848 (mt) REVERT: D 312 GLN cc_start: 0.7831 (mt0) cc_final: 0.7607 (mm-40) REVERT: F 42 PHE cc_start: 0.8556 (m-80) cc_final: 0.8146 (m-80) REVERT: F 86 GLU cc_start: 0.7501 (mp0) cc_final: 0.7223 (mp0) REVERT: F 129 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7742 (mp-120) REVERT: F 180 MET cc_start: 0.8089 (mtp) cc_final: 0.7825 (mtm) REVERT: F 241 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7747 (m) REVERT: F 416 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7122 (tp30) REVERT: F 449 SER cc_start: 0.7477 (t) cc_final: 0.7250 (m) REVERT: F 475 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8180 (ttm170) outliers start: 29 outliers final: 14 residues processed: 387 average time/residue: 0.6430 time to fit residues: 270.8421 Evaluate side-chains 389 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 371 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 416 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 145 optimal weight: 0.1980 chunk 130 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 89 optimal weight: 0.0060 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 210 ASN C 120 GLN C 200 GLN C 201 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.126637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116926 restraints weight = 17617.055| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.51 r_work: 0.3491 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14227 Z= 0.151 Angle : 0.626 15.707 19358 Z= 0.300 Chirality : 0.044 0.162 2177 Planarity : 0.005 0.050 2477 Dihedral : 6.757 169.536 1996 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.89 % Allowed : 22.32 % Favored : 75.79 % 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: 0.74 (0.20), residues: 1763 helix: 1.07 (0.18), residues: 864 sheet: -0.55 (0.39), residues: 180 loop : 0.24 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 146 TYR 0.022 0.002 TYR F 140 PHE 0.030 0.002 PHE B 44 TRP 0.015 0.001 TRP A 293 HIS 0.004 0.001 HIS F 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (14218) covalent geometry : angle 0.59096 / 0.30 (19332) SS BOND : bond 0.00277 / 0.15 ( 1) SS BOND : angle 1.38354 / 0.81 ( 2) hydrogen bonds : bond 0.03712 / 2.55 ( 703) hydrogen bonds : angle 4.90438 / 3.66 ( 2061) metal coordination : bond 0.00871 / 0.37 ( 8) metal coordination : angle 5.91427 / 3.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 371 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8400 (tpp) cc_final: 0.8082 (tpt) REVERT: A 248 MET cc_start: 0.7936 (mmm) cc_final: 0.7699 (tpp) REVERT: A 313 VAL cc_start: 0.8090 (t) cc_final: 0.7798 (m) REVERT: B 228 SER cc_start: 0.7874 (t) cc_final: 0.7597 (p) REVERT: C 117 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7566 (ttpt) REVERT: C 203 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7384 (mt-10) REVERT: C 241 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7905 (tt) REVERT: C 255 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7552 (mmm-85) REVERT: C 265 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6661 (mm-30) REVERT: D 33 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7492 (mtp85) REVERT: D 176 LEU cc_start: 0.8897 (mt) cc_final: 0.8660 (mt) REVERT: D 249 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7897 (mt) REVERT: F 42 PHE cc_start: 0.8589 (m-80) cc_final: 0.8174 (m-80) REVERT: F 86 GLU cc_start: 0.7537 (mp0) cc_final: 0.7193 (mp0) REVERT: F 129 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7759 (mp-120) REVERT: F 146 MET cc_start: 0.8057 (mtp) cc_final: 0.7726 (mtm) REVERT: F 180 MET cc_start: 0.8088 (mtp) cc_final: 0.7839 (mtm) REVERT: F 241 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7746 (m) REVERT: F 420 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7669 (mtt90) REVERT: F 449 SER cc_start: 0.7498 (t) cc_final: 0.7262 (m) REVERT: F 475 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8227 (ttm170) outliers start: 28 outliers final: 18 residues processed: 379 average time/residue: 0.6790 time to fit residues: 279.5989 Evaluate side-chains 385 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 364 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 137 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 136 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 210 ASN B 263 GLN C 201 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.125299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.116041 restraints weight = 17810.269| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.45 r_work: 0.3494 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14227 Z= 0.181 Angle : 0.676 17.131 19358 Z= 0.321 Chirality : 0.045 0.206 2177 Planarity : 0.005 0.049 2477 Dihedral : 6.821 168.354 1996 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.89 % Allowed : 22.45 % Favored : 75.66 % 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: 0.65 (0.20), residues: 1763 helix: 1.00 (0.18), residues: 865 sheet: -0.63 (0.38), residues: 180 loop : 0.21 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 146 TYR 0.023 0.002 TYR C 317 PHE 0.031 0.002 PHE B 44 TRP 0.014 0.001 TRP A 293 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (14218) covalent geometry : angle 0.64090 / 0.32 (19332) SS BOND : bond 0.00439 / 0.23 ( 1) SS BOND : angle 1.37321 / 0.81 ( 2) hydrogen bonds : bond 0.03877 / 2.65 ( 703) hydrogen bonds : angle 4.98173 / 3.72 ( 2061) metal coordination : bond 0.00991 / 0.43 ( 8) metal coordination : angle 6.08769 / 3.14 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 370 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.8370 (tpp) cc_final: 0.8034 (tpt) REVERT: B 228 SER cc_start: 0.7875 (t) cc_final: 0.7614 (p) REVERT: B 291 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7831 (ttp80) REVERT: C 117 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7553 (ttpt) REVERT: C 203 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 255 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7543 (mmm-85) REVERT: C 265 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6701 (mm-30) REVERT: D 25 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7855 (mtpm) REVERT: D 33 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7535 (mtp85) REVERT: D 176 LEU cc_start: 0.8918 (mt) cc_final: 0.8690 (mt) REVERT: D 249 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7903 (mt) REVERT: F 42 PHE cc_start: 0.8574 (m-80) cc_final: 0.8140 (m-80) REVERT: F 86 GLU cc_start: 0.7489 (mp0) cc_final: 0.7166 (mp0) REVERT: F 129 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7731 (mp-120) REVERT: F 146 MET cc_start: 0.8041 (mtp) cc_final: 0.7693 (mtm) REVERT: F 180 MET cc_start: 0.8095 (mtp) cc_final: 0.7859 (mtm) REVERT: F 241 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7699 (m) REVERT: F 449 SER cc_start: 0.7476 (t) cc_final: 0.7273 (m) REVERT: F 475 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8216 (ttm170) outliers start: 28 outliers final: 18 residues processed: 377 average time/residue: 0.6259 time to fit residues: 256.6195 Evaluate side-chains 388 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 367 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 419 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 38 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 126 optimal weight: 0.0870 chunk 113 optimal weight: 0.9980 chunk 68 optimal weight: 0.0270 chunk 153 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 210 ASN C 201 GLN F 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.127681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118034 restraints weight = 17496.925| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.51 r_work: 0.3498 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14227 Z= 0.121 Angle : 0.628 17.849 19358 Z= 0.300 Chirality : 0.043 0.159 2177 Planarity : 0.005 0.048 2477 Dihedral : 6.636 166.305 1996 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.55 % Allowed : 22.72 % Favored : 75.72 % 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: 0.84 (0.21), residues: 1763 helix: 1.19 (0.18), residues: 861 sheet: -0.68 (0.38), residues: 184 loop : 0.30 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 420 TYR 0.017 0.002 TYR C 317 PHE 0.031 0.001 PHE B 44 TRP 0.018 0.001 TRP A 293 HIS 0.004 0.001 HIS F 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (14218) covalent geometry : angle 0.59374 / 0.30 (19332) SS BOND : bond 0.00170 / 0.09 ( 1) SS BOND : angle 1.25709 / 0.74 ( 2) hydrogen bonds : bond 0.03511 / 2.40 ( 703) hydrogen bonds : angle 4.89588 / 3.65 ( 2061) metal coordination : bond 0.00667 / 0.28 ( 8) metal coordination : angle 5.82675 / 3.04 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5812.97 seconds wall clock time: 99 minutes 36.77 seconds (5976.77 seconds total)