Starting phenix.real_space_refine on Thu Jun 12 14:20:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1y_39740/06_2025/8z1y_39740_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1y_39740/06_2025/8z1y_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_39740/06_2025/8z1y_39740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1y_39740/06_2025/8z1y_39740.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1y_39740/06_2025/8z1y_39740_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1y_39740/06_2025/8z1y_39740_neut.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.96, per 1000 atoms: 0.64 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: 3.49 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.56 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: 3.93 Time building geometry restraints manager: 4.09 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 - 2.38: 15336 2.38 - 4.76: 3613 4.76 - 7.14: 317 7.14 - 9.52: 52 9.52 - 11.90: 14 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=" C4 AGS D 402 " pdb=" C5 AGS D 402 " pdb=" N7 AGS D 402 " ideal model delta sigma weight residual 110.73 114.04 -3.31 4.52e-01 4.89e+00 5.35e+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=" C4 AGS C 401 " pdb=" C5 AGS C 401 " pdb=" N7 AGS C 401 " ideal model delta sigma weight residual 110.73 113.89 -3.16 4.52e-01 4.89e+00 4.88e+01 ... (remaining 19327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 8386 31.27 - 62.54: 174 62.54 - 93.81: 13 93.81 - 125.08: 1 125.08 - 156.36: 1 Dihedral angle restraints: 8575 sinusoidal: 3472 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 8572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1882 0.161 - 0.321: 196 0.321 - 0.482: 41 0.482 - 0.642: 49 0.642 - 0.802: 13 Chirality restraints: 2181 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 2178 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: 3.440 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.040 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 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= 0.918 Angle : 1.978 17.876 19358 Z= 1.320 Chirality : 0.146 0.802 2181 Planarity : 0.016 0.123 2477 Dihedral : 13.056 156.355 5296 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.088 0.024 TRP F 433 HIS 0.016 0.004 HIS C 212 PHE 0.097 0.015 PHE A 24 TYR 0.189 0.022 TYR F 132 ARG 0.012 0.002 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.17024 ( 703) hydrogen bonds : angle 7.80604 ( 2061) metal coordination : bond 0.09776 ( 8) metal coordination : angle 7.44358 ( 24) SS BOND : bond 0.01324 ( 1) SS BOND : angle 3.72086 ( 2) covalent geometry : bond 0.01589 (14218) covalent geometry : angle 1.96167 (19332) *********************** 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 : 1.706 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: 0.6901 (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: 0.7133 (p) REVERT: A 247 ARG cc_start: 0.6669 (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: 0.6975 (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: 0.7400 (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: 0.7786 (mt0) REVERT: C 173 LYS cc_start: 0.7229 (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: 0.7825 (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: 0.7954 (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: 0.7231 (ptt-90) REVERT: D 312 GLN cc_start: 0.7345 (mt0) cc_final: 0.6946 (mt0) REVERT: F 66 GLU cc_start: 0.7426 (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: 0.6870 (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: 0.6764 (tpt) REVERT: F 201 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6249 (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: 0.6915 (mtp) REVERT: F 406 GLN cc_start: 0.7798 (mt0) cc_final: 0.7491 (mt0) REVERT: F 419 LYS cc_start: 0.7174 (tttp) cc_final: 0.6824 (ttpp) REVERT: F 420 ARG cc_start: 0.7258 (mtt-85) cc_final: 0.7029 (mtt90) REVERT: F 423 ASP cc_start: 0.7133 (t0) cc_final: 0.6700 (t0) 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: 1.4361 time to fit residues: 705.2703 Evaluate side-chains 400 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 102 optimal weight: 0.0270 chunk 158 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3716 r_free = 0.3716 target = 0.126527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117224 restraints weight = 17660.025| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.44 r_work: 0.3500 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14227 Z= 0.166 Angle : 0.684 15.721 19358 Z= 0.345 Chirality : 0.047 0.237 2181 Planarity : 0.005 0.051 2477 Dihedral : 7.852 152.708 1960 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.69 % Allowed : 10.99 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1763 helix: 0.34 (0.17), residues: 868 sheet: -0.68 (0.39), residues: 159 loop : 0.20 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 293 HIS 0.007 0.001 HIS C 119 PHE 0.023 0.002 PHE F 107 TYR 0.021 0.002 TYR F 417 ARG 0.007 0.001 ARG D 298 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 703) hydrogen bonds : angle 5.52002 ( 2061) metal coordination : bond 0.01019 ( 8) metal coordination : angle 6.28295 ( 24) SS BOND : bond 0.00263 ( 1) SS BOND : angle 2.75449 ( 2) covalent geometry : bond 0.00385 (14218) covalent geometry : angle 0.64741 (19332) *********************** 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 407 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 382 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8066 (tpp) cc_final: 0.7857 (tpt) REVERT: A 52 LEU cc_start: 0.8270 (mt) cc_final: 0.8011 (mt) REVERT: A 56 LEU cc_start: 0.8292 (mt) cc_final: 0.8026 (mp) REVERT: A 205 MET cc_start: 0.8065 (tpp) cc_final: 0.7830 (mmm) REVERT: A 223 MET cc_start: 0.8330 (tpp) cc_final: 0.7986 (tpt) REVERT: A 251 ILE cc_start: 0.8101 (mt) cc_final: 0.7885 (mm) REVERT: B 205 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7584 (ttt90) REVERT: C 34 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: C 44 SER cc_start: 0.7562 (m) cc_final: 0.7341 (p) REVERT: C 73 GLN cc_start: 0.7794 (mp-120) cc_final: 0.7458 (mp-120) REVERT: C 117 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7713 (ttpt) REVERT: C 137 GLN cc_start: 0.7972 (mt0) cc_final: 0.7739 (mt0) REVERT: C 179 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: C 189 GLN cc_start: 0.8335 (tt0) cc_final: 0.8090 (tt0) REVERT: C 203 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7453 (mt-10) REVERT: C 227 MET cc_start: 0.8190 (ttm) cc_final: 0.7933 (mtt) REVERT: D 49 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8352 (mttp) REVERT: D 195 SER cc_start: 0.7965 (t) cc_final: 0.7724 (m) REVERT: D 226 GLU cc_start: 0.7813 (tt0) cc_final: 0.7605 (tt0) REVERT: D 312 GLN cc_start: 0.7747 (mt0) cc_final: 0.7513 (mt0) REVERT: F 54 ASP cc_start: 0.7609 (m-30) cc_final: 0.7381 (m-30) REVERT: F 100 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7986 (ptpp) REVERT: F 106 GLU cc_start: 0.6840 (pt0) cc_final: 0.6603 (pt0) REVERT: F 129 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7543 (mp-120) REVERT: F 146 MET cc_start: 0.7948 (mmm) cc_final: 0.7603 (mmm) REVERT: F 180 MET cc_start: 0.8104 (mtp) cc_final: 0.7902 (mtm) REVERT: F 342 MET cc_start: 0.8474 (ttm) cc_final: 0.8224 (ttp) REVERT: F 395 MET cc_start: 0.8342 (mtm) cc_final: 0.7999 (mtp) REVERT: F 430 MET cc_start: 0.7826 (mmt) cc_final: 0.7521 (mmm) outliers start: 25 outliers final: 9 residues processed: 385 average time/residue: 1.4147 time to fit residues: 589.2212 Evaluate side-chains 362 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 350 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 SER 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 281 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 130 optimal weight: 0.0980 chunk 143 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 129 optimal weight: 0.0670 chunk 5 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 159 optimal weight: 0.0670 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 60 GLN B 210 ASN C 120 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117762 restraints weight = 17744.483| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.44 r_work: 0.3501 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14227 Z= 0.141 Angle : 0.616 15.128 19358 Z= 0.303 Chirality : 0.044 0.245 2181 Planarity : 0.005 0.051 2477 Dihedral : 7.179 135.586 1960 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.03 % Allowed : 13.96 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1763 helix: 0.73 (0.18), residues: 872 sheet: -0.64 (0.36), residues: 187 loop : 0.33 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 293 HIS 0.006 0.001 HIS C 212 PHE 0.019 0.002 PHE B 283 TYR 0.017 0.002 TYR F 267 ARG 0.007 0.001 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 703) hydrogen bonds : angle 5.11673 ( 2061) metal coordination : bond 0.00832 ( 8) metal coordination : angle 5.91713 ( 24) SS BOND : bond 0.00264 ( 1) SS BOND : angle 2.04165 ( 2) covalent geometry : bond 0.00331 (14218) covalent geometry : angle 0.58010 (19332) *********************** 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 403 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 358 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8336 (mt) cc_final: 0.7996 (mt) REVERT: A 56 LEU cc_start: 0.8294 (mt) cc_final: 0.8070 (mp) REVERT: A 205 MET cc_start: 0.8013 (tpp) cc_final: 0.7812 (mmm) REVERT: A 223 MET cc_start: 0.8329 (tpp) cc_final: 0.8064 (tpt) REVERT: A 325 ASP cc_start: 0.7730 (t0) cc_final: 0.7506 (m-30) REVERT: B 22 PHE cc_start: 0.7823 (t80) cc_final: 0.7590 (t80) REVERT: B 205 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7513 (ttt90) REVERT: B 228 SER cc_start: 0.7832 (t) cc_final: 0.7576 (p) REVERT: C 66 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7574 (mt-10) REVERT: C 101 SER cc_start: 0.7752 (t) cc_final: 0.7540 (p) REVERT: C 117 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7650 (ttpt) REVERT: C 203 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7494 (mt-10) REVERT: C 227 MET cc_start: 0.8313 (ttm) cc_final: 0.8059 (mtt) REVERT: D 133 SER cc_start: 0.7261 (OUTLIER) cc_final: 0.7046 (p) REVERT: D 285 SER cc_start: 0.8097 (t) cc_final: 0.7794 (p) REVERT: D 300 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7274 (ptt-90) REVERT: D 312 GLN cc_start: 0.7772 (mt0) cc_final: 0.7564 (mt0) REVERT: F 129 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7626 (mp-120) REVERT: F 146 MET cc_start: 0.7899 (mmm) cc_final: 0.7581 (mmm) REVERT: F 202 LYS cc_start: 0.7751 (mttt) cc_final: 0.7519 (ttmm) REVERT: F 420 ARG cc_start: 0.8073 (mtt-85) cc_final: 0.7867 (mtt90) REVERT: F 425 GLU cc_start: 0.7402 (tt0) cc_final: 0.7183 (tt0) REVERT: F 430 MET cc_start: 0.7835 (mmt) cc_final: 0.7541 (mmm) REVERT: F 449 SER cc_start: 0.7657 (t) cc_final: 0.7375 (m) REVERT: F 470 LEU cc_start: 0.8470 (mt) cc_final: 0.8226 (mp) outliers start: 45 outliers final: 15 residues processed: 367 average time/residue: 1.4104 time to fit residues: 560.8535 Evaluate side-chains 364 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 347 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 271 VAL 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 67 LYS Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain D residue 133 SER 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 Chi-restraints excluded: chain F residue 357 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 0.0570 chunk 4 optimal weight: 0.1980 chunk 116 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 20 GLN B 60 GLN B 210 ASN C 120 GLN C 179 GLN C 189 GLN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN F 114 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.126555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117254 restraints weight = 17603.428| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.45 r_work: 0.3497 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2704 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= 0.134 Angle : 0.601 14.545 19358 Z= 0.292 Chirality : 0.043 0.254 2181 Planarity : 0.004 0.045 2477 Dihedral : 6.884 129.174 1960 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.24 % Allowed : 15.17 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1763 helix: 0.88 (0.17), residues: 872 sheet: -0.55 (0.38), residues: 183 loop : 0.31 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 293 HIS 0.005 0.001 HIS F 426 PHE 0.024 0.001 PHE F 107 TYR 0.014 0.002 TYR F 267 ARG 0.005 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 703) hydrogen bonds : angle 5.00166 ( 2061) metal coordination : bond 0.00718 ( 8) metal coordination : angle 5.74577 ( 24) SS BOND : bond 0.00208 ( 1) SS BOND : angle 1.72899 ( 2) covalent geometry : bond 0.00313 (14218) covalent geometry : angle 0.56558 (19332) *********************** 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 421 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 373 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8289 (mt) cc_final: 0.7933 (mt) REVERT: A 223 MET cc_start: 0.8332 (tpp) cc_final: 0.7969 (tpt) REVERT: A 325 ASP cc_start: 0.7776 (t0) cc_final: 0.7553 (m-30) REVERT: B 22 PHE cc_start: 0.7832 (t80) cc_final: 0.7627 (t80) REVERT: B 62 ARG cc_start: 0.8438 (mmt90) cc_final: 0.7956 (mpt-90) REVERT: B 205 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7508 (ttt90) REVERT: B 228 SER cc_start: 0.7850 (t) cc_final: 0.7624 (p) REVERT: C 66 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7633 (mt-10) REVERT: C 117 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7635 (ttpt) REVERT: C 203 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7456 (mt-10) REVERT: C 227 MET cc_start: 0.8356 (ttm) cc_final: 0.8122 (mtt) REVERT: C 241 ILE cc_start: 0.8274 (mm) cc_final: 0.8054 (tt) REVERT: C 265 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6662 (mm-30) REVERT: D 33 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7183 (ttp80) REVERT: D 36 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7835 (mppt) REVERT: D 195 SER cc_start: 0.7853 (t) cc_final: 0.7643 (m) REVERT: D 300 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7297 (ptt-90) REVERT: D 312 GLN cc_start: 0.7770 (mt0) cc_final: 0.7570 (mt0) REVERT: F 129 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7675 (mp-120) REVERT: F 342 MET cc_start: 0.8537 (ttm) cc_final: 0.8284 (ttp) REVERT: F 425 GLU cc_start: 0.7450 (tt0) cc_final: 0.7236 (tt0) REVERT: F 430 MET cc_start: 0.7741 (mmt) cc_final: 0.7348 (mmm) REVERT: F 449 SER cc_start: 0.7615 (t) cc_final: 0.7349 (m) outliers start: 48 outliers final: 22 residues processed: 385 average time/residue: 1.5249 time to fit residues: 635.7985 Evaluate side-chains 386 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 361 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET 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 256 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 230 ASP 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 Chi-restraints excluded: chain F residue 357 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 101 optimal weight: 0.0870 chunk 82 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 210 ASN C 120 GLN C 179 GLN C 201 GLN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN D 187 GLN D 227 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.125822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.116223 restraints weight = 17730.394| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.52 r_work: 0.3480 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14227 Z= 0.179 Angle : 0.631 16.950 19358 Z= 0.304 Chirality : 0.045 0.264 2181 Planarity : 0.005 0.049 2477 Dihedral : 6.823 124.676 1960 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.57 % Allowed : 17.19 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1763 helix: 0.86 (0.17), residues: 869 sheet: -0.64 (0.37), residues: 184 loop : 0.22 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.005 0.001 HIS A 254 PHE 0.029 0.002 PHE F 107 TYR 0.016 0.002 TYR D 155 ARG 0.012 0.001 ARG F 420 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 703) hydrogen bonds : angle 5.00518 ( 2061) metal coordination : bond 0.01082 ( 8) metal coordination : angle 6.08408 ( 24) SS BOND : bond 0.00377 ( 1) SS BOND : angle 1.67640 ( 2) covalent geometry : bond 0.00434 (14218) covalent geometry : angle 0.59364 (19332) *********************** 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: 53 poor density : 382 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8339 (tpp) cc_final: 0.8053 (tpt) REVERT: B 22 PHE cc_start: 0.7881 (t80) cc_final: 0.7663 (t80) REVERT: B 62 ARG cc_start: 0.8385 (mmt90) cc_final: 0.8054 (mpt-90) REVERT: B 205 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7503 (ttt90) REVERT: B 228 SER cc_start: 0.7921 (t) cc_final: 0.7666 (p) REVERT: C 66 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7687 (mt-10) REVERT: C 117 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7678 (ttpt) REVERT: C 203 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7432 (mt-10) REVERT: C 241 ILE cc_start: 0.8334 (mm) cc_final: 0.8090 (tt) REVERT: C 265 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6714 (mm-30) REVERT: D 33 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7176 (ttp80) REVERT: D 195 SER cc_start: 0.7866 (t) cc_final: 0.7654 (m) REVERT: D 267 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7518 (tpp-160) REVERT: D 279 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7241 (mm) REVERT: D 298 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7369 (ptm160) REVERT: D 300 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7327 (ptt-90) REVERT: D 312 GLN cc_start: 0.7871 (mt0) cc_final: 0.7655 (mt0) REVERT: F 129 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7734 (mp-120) REVERT: F 180 MET cc_start: 0.8044 (mtp) cc_final: 0.7834 (mtm) REVERT: F 430 MET cc_start: 0.7756 (mmt) cc_final: 0.7328 (mmm) REVERT: F 449 SER cc_start: 0.7606 (t) cc_final: 0.7347 (m) REVERT: F 475 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8110 (ttm170) outliers start: 53 outliers final: 22 residues processed: 397 average time/residue: 1.3598 time to fit residues: 587.1613 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 : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 247 ARG 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 256 SER 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 67 LYS Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 298 ARG 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 287 MET Chi-restraints excluded: chain F residue 357 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 79 HIS B 210 ASN B 214 ASN C 120 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 201 GLN C 231 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN F 114 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.124426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115247 restraints weight = 17888.945| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.43 r_work: 0.3474 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14227 Z= 0.234 Angle : 0.670 19.577 19358 Z= 0.321 Chirality : 0.047 0.260 2181 Planarity : 0.005 0.053 2477 Dihedral : 6.898 122.517 1960 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.84 % Allowed : 18.34 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1763 helix: 0.74 (0.17), residues: 868 sheet: -0.69 (0.37), residues: 184 loop : 0.13 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 293 HIS 0.006 0.001 HIS A 254 PHE 0.031 0.002 PHE F 107 TYR 0.021 0.002 TYR C 317 ARG 0.010 0.001 ARG F 420 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 703) hydrogen bonds : angle 5.08778 ( 2061) metal coordination : bond 0.01332 ( 8) metal coordination : angle 6.55996 ( 24) SS BOND : bond 0.00510 ( 1) SS BOND : angle 1.54848 ( 2) covalent geometry : bond 0.00574 (14218) covalent geometry : angle 0.62960 (19332) *********************** 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 428 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 371 time to evaluate : 2.204 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.8327 (tpp) cc_final: 0.8041 (tpt) REVERT: B 62 ARG cc_start: 0.8442 (mmt90) cc_final: 0.8071 (mpt-90) REVERT: B 205 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7544 (ttt-90) REVERT: B 228 SER cc_start: 0.7951 (t) cc_final: 0.7713 (p) REVERT: C 66 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7718 (mt-10) REVERT: C 117 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7674 (ttpt) REVERT: C 129 GLN cc_start: 0.7844 (tp40) cc_final: 0.7490 (tp40) REVERT: C 203 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7412 (mt-10) REVERT: C 241 ILE cc_start: 0.8367 (mm) cc_final: 0.8122 (tt) REVERT: C 255 ARG cc_start: 0.7800 (ttm170) cc_final: 0.7558 (tpp-160) REVERT: C 265 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6745 (mm-30) REVERT: D 33 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7184 (ttp80) REVERT: D 279 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7302 (mp) REVERT: D 285 SER cc_start: 0.8249 (t) cc_final: 0.8037 (p) REVERT: D 298 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7293 (ptm160) REVERT: D 300 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7299 (ptt-90) REVERT: D 312 GLN cc_start: 0.7845 (mt0) cc_final: 0.7626 (mt0) REVERT: F 86 GLU cc_start: 0.7561 (mp0) cc_final: 0.7220 (mp0) REVERT: F 106 GLU cc_start: 0.6946 (pt0) cc_final: 0.6691 (pt0) REVERT: F 129 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7702 (mp-120) REVERT: F 388 ASN cc_start: 0.8444 (t160) cc_final: 0.8213 (t160) REVERT: F 430 MET cc_start: 0.7720 (mmt) cc_final: 0.7362 (mmm) REVERT: F 449 SER cc_start: 0.7605 (t) cc_final: 0.7349 (m) REVERT: F 475 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8179 (ttm170) outliers start: 57 outliers final: 29 residues processed: 394 average time/residue: 1.5853 time to fit residues: 677.9577 Evaluate side-chains 391 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 358 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET 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 143 MET Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 271 VAL 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 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 96 GLN 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 211 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 298 ARG 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 338 ILE Chi-restraints excluded: chain F residue 357 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 25 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 24 optimal weight: 0.0770 chunk 129 optimal weight: 0.9980 chunk 166 optimal weight: 0.3980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 210 ASN C 120 GLN C 179 GLN C 251 GLN D 187 GLN F 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.125791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.116538 restraints weight = 17759.994| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.44 r_work: 0.3491 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14227 Z= 0.149 Angle : 0.620 17.673 19358 Z= 0.298 Chirality : 0.044 0.262 2181 Planarity : 0.005 0.047 2477 Dihedral : 6.723 120.015 1960 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.24 % Allowed : 20.03 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1763 helix: 0.94 (0.18), residues: 866 sheet: -0.65 (0.38), residues: 184 loop : 0.22 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 293 HIS 0.004 0.001 HIS C 119 PHE 0.033 0.002 PHE F 107 TYR 0.018 0.002 TYR F 140 ARG 0.006 0.001 ARG F 420 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 703) hydrogen bonds : angle 4.99448 ( 2061) metal coordination : bond 0.00901 ( 8) metal coordination : angle 6.20967 ( 24) SS BOND : bond 0.00302 ( 1) SS BOND : angle 1.51235 ( 2) covalent geometry : bond 0.00355 (14218) covalent geometry : angle 0.58037 (19332) *********************** 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 421 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 373 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.8338 (tpp) cc_final: 0.8045 (tpt) REVERT: B 205 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7441 (ttt-90) REVERT: B 228 SER cc_start: 0.7889 (t) cc_final: 0.7661 (p) REVERT: C 66 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7685 (mt-10) REVERT: C 117 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7665 (ttpt) REVERT: C 203 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 241 ILE cc_start: 0.8253 (mm) cc_final: 0.8019 (tt) REVERT: C 265 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6712 (mm-30) REVERT: D 33 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7488 (mtp85) REVERT: D 36 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7883 (mppt) REVERT: D 61 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7956 (mppt) REVERT: D 176 LEU cc_start: 0.8937 (mt) cc_final: 0.8715 (mt) REVERT: D 279 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7325 (mm) REVERT: D 298 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7316 (ptm160) REVERT: D 312 GLN cc_start: 0.7859 (mt0) cc_final: 0.7642 (mt0) REVERT: F 86 GLU cc_start: 0.7548 (mp0) cc_final: 0.7200 (mp0) REVERT: F 129 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7683 (mp-120) REVERT: F 241 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7713 (m) REVERT: F 388 ASN cc_start: 0.8376 (t160) cc_final: 0.8168 (t160) REVERT: F 430 MET cc_start: 0.7678 (mmt) cc_final: 0.7364 (mmm) REVERT: F 449 SER cc_start: 0.7554 (t) cc_final: 0.7301 (m) REVERT: F 475 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8185 (ttm170) outliers start: 48 outliers final: 20 residues processed: 388 average time/residue: 1.4793 time to fit residues: 622.6807 Evaluate side-chains 386 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 360 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 96 GLN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 298 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 241 THR Chi-restraints excluded: chain F residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 130 optimal weight: 0.7980 chunk 17 optimal weight: 0.0070 chunk 120 optimal weight: 0.0060 chunk 53 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 85 optimal weight: 0.0980 chunk 116 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 210 ASN C 120 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 187 GLN F 114 ASN F 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116450 restraints weight = 17770.261| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.55 r_work: 0.3495 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14227 Z= 0.128 Angle : 0.607 15.686 19358 Z= 0.291 Chirality : 0.043 0.263 2181 Planarity : 0.005 0.047 2477 Dihedral : 6.571 118.925 1960 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.63 % Allowed : 20.77 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1763 helix: 1.07 (0.18), residues: 861 sheet: -0.56 (0.38), residues: 190 loop : 0.31 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 293 HIS 0.005 0.001 HIS C 212 PHE 0.036 0.001 PHE F 107 TYR 0.017 0.002 TYR C 317 ARG 0.009 0.001 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 703) hydrogen bonds : angle 4.90016 ( 2061) metal coordination : bond 0.00730 ( 8) metal coordination : angle 5.92156 ( 24) SS BOND : bond 0.00198 ( 1) SS BOND : angle 1.37645 ( 2) covalent geometry : bond 0.00300 (14218) covalent geometry : angle 0.57074 (19332) *********************** 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 410 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 371 time to evaluate : 3.599 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.8042 (tpp) cc_final: 0.7838 (mmm) REVERT: A 223 MET cc_start: 0.8370 (tpp) cc_final: 0.8050 (tpt) REVERT: B 205 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7449 (ttt90) REVERT: B 228 SER cc_start: 0.7858 (t) cc_final: 0.7607 (p) REVERT: B 291 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7931 (ttp80) REVERT: C 66 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 117 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7621 (ttpt) REVERT: C 203 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7393 (mt-10) REVERT: C 241 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7929 (tt) REVERT: C 265 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6737 (mm-30) REVERT: D 33 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7456 (mtp85) REVERT: D 36 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7883 (mppt) REVERT: D 61 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7936 (mppt) REVERT: D 176 LEU cc_start: 0.8880 (mt) cc_final: 0.8648 (mt) REVERT: D 279 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7297 (mm) REVERT: D 298 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7377 (ptm160) REVERT: D 312 GLN cc_start: 0.7969 (mt0) cc_final: 0.7740 (mm-40) REVERT: F 86 GLU cc_start: 0.7605 (mp0) cc_final: 0.7321 (mp0) REVERT: F 129 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7756 (mp-120) REVERT: F 202 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7582 (ttpt) REVERT: F 241 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7757 (m) REVERT: F 388 ASN cc_start: 0.8390 (t160) cc_final: 0.8180 (t160) REVERT: F 420 ARG cc_start: 0.7823 (mtt90) cc_final: 0.7576 (mtt-85) REVERT: F 449 SER cc_start: 0.7531 (t) cc_final: 0.7292 (m) REVERT: F 475 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8211 (ttm170) outliers start: 39 outliers final: 17 residues processed: 386 average time/residue: 1.7139 time to fit residues: 719.7899 Evaluate side-chains 390 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 366 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 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 67 LYS Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 148 ASP 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 33 ARG Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 298 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 122 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 15 optimal weight: 0.0970 chunk 90 optimal weight: 0.4980 chunk 93 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 0.0970 chunk 91 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 210 ASN C 120 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN D 252 ASN F 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.116771 restraints weight = 17477.590| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.52 r_work: 0.3487 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3322 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= 0.138 Angle : 0.625 15.462 19358 Z= 0.298 Chirality : 0.043 0.165 2181 Planarity : 0.005 0.047 2477 Dihedral : 6.537 118.662 1960 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.82 % Allowed : 21.65 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1763 helix: 1.11 (0.18), residues: 861 sheet: -0.51 (0.38), residues: 190 loop : 0.32 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.005 0.001 HIS C 212 PHE 0.037 0.001 PHE F 107 TYR 0.021 0.002 TYR F 140 ARG 0.007 0.001 ARG F 169 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 703) hydrogen bonds : angle 4.89050 ( 2061) metal coordination : bond 0.00788 ( 8) metal coordination : angle 5.85655 ( 24) SS BOND : bond 0.00239 ( 1) SS BOND : angle 1.31852 ( 2) covalent geometry : bond 0.00330 (14218) covalent geometry : angle 0.59041 (19332) *********************** 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 391 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 364 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.8353 (tpp) cc_final: 0.8038 (tpt) REVERT: B 205 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7434 (ttt90) REVERT: B 228 SER cc_start: 0.7853 (t) cc_final: 0.7601 (p) REVERT: B 291 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7924 (ttp80) REVERT: C 66 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7708 (mt-10) REVERT: C 117 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7631 (ttpt) REVERT: C 203 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7388 (mt-10) REVERT: C 241 ILE cc_start: 0.8148 (mm) cc_final: 0.7909 (tt) REVERT: C 265 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6730 (mm-30) REVERT: D 33 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7454 (mtp85) REVERT: D 36 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7923 (mppt) REVERT: D 61 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7939 (mppt) REVERT: D 176 LEU cc_start: 0.8882 (mt) cc_final: 0.8648 (mt) REVERT: D 312 GLN cc_start: 0.7963 (mt0) cc_final: 0.7731 (mm-40) REVERT: F 86 GLU cc_start: 0.7572 (mp0) cc_final: 0.7292 (mp0) REVERT: F 129 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7717 (mp-120) REVERT: F 202 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7582 (ttpt) REVERT: F 241 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7747 (m) REVERT: F 388 ASN cc_start: 0.8385 (t160) cc_final: 0.8159 (t160) REVERT: F 449 SER cc_start: 0.7531 (t) cc_final: 0.7285 (m) REVERT: F 475 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8207 (ttm170) outliers start: 27 outliers final: 14 residues processed: 375 average time/residue: 1.4354 time to fit residues: 586.1281 Evaluate side-chains 383 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 365 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER 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 67 LYS Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 230 ASP 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 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 90 optimal weight: 0.0470 chunk 69 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 102 optimal weight: 0.0670 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 210 ASN C 120 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN F 531 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.126685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116926 restraints weight = 17621.210| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.52 r_work: 0.3498 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14227 Z= 0.137 Angle : 0.613 15.152 19358 Z= 0.296 Chirality : 0.043 0.163 2181 Planarity : 0.005 0.046 2477 Dihedral : 6.525 118.048 1960 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.75 % Allowed : 21.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1763 helix: 1.16 (0.18), residues: 861 sheet: -0.50 (0.38), residues: 190 loop : 0.32 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.006 0.001 HIS C 212 PHE 0.037 0.002 PHE F 107 TYR 0.019 0.002 TYR C 317 ARG 0.008 0.001 ARG F 169 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 703) hydrogen bonds : angle 4.88089 ( 2061) metal coordination : bond 0.00781 ( 8) metal coordination : angle 5.72253 ( 24) SS BOND : bond 0.00274 ( 1) SS BOND : angle 1.26453 ( 2) covalent geometry : bond 0.00327 (14218) covalent geometry : angle 0.57961 (19332) ********************** 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 399 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 373 time to evaluate : 1.403 Fit side-chains REVERT: A 205 MET cc_start: 0.8020 (tpp) cc_final: 0.7819 (mmm) REVERT: A 223 MET cc_start: 0.8367 (tpp) cc_final: 0.8031 (tpt) REVERT: B 205 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7466 (ttt90) REVERT: B 228 SER cc_start: 0.7847 (t) cc_final: 0.7602 (p) REVERT: C 66 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 117 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7605 (ttpt) REVERT: C 203 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7370 (mt-10) REVERT: C 265 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6740 (mm-30) REVERT: D 33 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7429 (mtp85) REVERT: D 36 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7911 (mppt) REVERT: D 61 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7934 (mppt) REVERT: D 176 LEU cc_start: 0.8881 (mt) cc_final: 0.8655 (mt) REVERT: D 312 GLN cc_start: 0.7997 (mt0) cc_final: 0.7788 (mm-40) REVERT: F 86 GLU cc_start: 0.7570 (mp0) cc_final: 0.7291 (mp0) REVERT: F 129 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7746 (mp-120) REVERT: F 202 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7643 (ttmm) REVERT: F 241 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7737 (m) REVERT: F 388 ASN cc_start: 0.8382 (t160) cc_final: 0.8178 (t160) REVERT: F 449 SER cc_start: 0.7500 (t) cc_final: 0.7267 (m) REVERT: F 475 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8216 (ttm170) outliers start: 26 outliers final: 15 residues processed: 386 average time/residue: 1.3701 time to fit residues: 573.9905 Evaluate side-chains 387 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 368 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 161 ILE 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 96 GLN Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 69 THR 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 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 62 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 0.0050 chunk 90 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 133 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 210 ASN B 263 GLN C 120 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 187 GLN F 531 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116615 restraints weight = 17704.791| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.53 r_work: 0.3492 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3436 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= 0.157 Angle : 0.646 16.184 19358 Z= 0.308 Chirality : 0.044 0.168 2181 Planarity : 0.005 0.053 2477 Dihedral : 6.547 118.192 1960 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.69 % Allowed : 22.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1763 helix: 1.12 (0.18), residues: 862 sheet: -0.50 (0.38), residues: 190 loop : 0.30 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 293 HIS 0.006 0.001 HIS C 212 PHE 0.034 0.002 PHE B 44 TYR 0.022 0.002 TYR F 354 ARG 0.005 0.001 ARG F 169 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 703) hydrogen bonds : angle 4.88763 ( 2061) metal coordination : bond 0.00889 ( 8) metal coordination : angle 5.78348 ( 24) SS BOND : bond 0.00344 ( 1) SS BOND : angle 1.25588 ( 2) covalent geometry : bond 0.00380 (14218) covalent geometry : angle 0.61378 (19332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12893.15 seconds wall clock time: 223 minutes 55.37 seconds (13435.37 seconds total)