Starting phenix.real_space_refine on Thu Sep 18 04:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1y_39740/09_2025/8z1y_39740_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1y_39740/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z1y_39740/09_2025/8z1y_39740_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1y_39740/09_2025/8z1y_39740_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z1y_39740/09_2025/8z1y_39740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1y_39740/09_2025/8z1y_39740.map" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 6 5.49 5 S 97 5.16 5 C 8885 2.51 5 N 2385 2.21 5 O 2516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13897 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2562 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 17, 'TRANS': 313} Chain: "B" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2187 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 17, 'TRANS': 271} Chain: "C" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2486 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 20, 'TRANS': 303} Chain: "D" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2537 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 22, 'TRANS': 299} Chain: "F" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4047 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 31, 'TRANS': 475} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'AGS': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'AGS': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6915 SG CYS C 284 31.671 22.952 136.390 1.00119.16 S ATOM 6963 SG CYS C 290 36.378 24.091 141.226 1.00 99.77 S ATOM 7019 SG CYS C 297 32.458 18.954 141.089 1.00135.73 S ATOM 7155 SG CYS C 315 30.081 24.869 142.406 1.00101.76 S ATOM 9586 SG CYS D 306 48.994 78.583 135.298 1.00123.84 S ATOM 9715 SG CYS D 323 51.547 73.100 137.713 1.00119.19 S ATOM 9479 SG CYS D 293 49.392 73.791 131.595 1.00113.07 S ATOM 9525 SG CYS D 299 45.114 73.565 136.781 1.00120.68 S Time building chain proxies: 3.43, per 1000 atoms: 0.25 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: 1.18 Conformation dependent library (CDL) restraints added in 607.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 402 " pdb="FE4 SF4 C 402 " - pdb=" SG CYS C 315 " pdb="FE2 SF4 C 402 " - pdb=" SG CYS C 290 " pdb="FE3 SF4 C 402 " - pdb=" SG CYS C 297 " pdb="FE1 SF4 C 402 " - pdb=" SG CYS C 284 " pdb=" SF4 D 401 " pdb="FE2 SF4 D 401 " - pdb=" SG CYS D 323 " pdb="FE3 SF4 D 401 " - pdb=" SG CYS D 293 " pdb="FE4 SF4 D 401 " - pdb=" SG CYS D 299 " pdb="FE1 SF4 D 401 " - pdb=" SG CYS D 306 " Number of angles added : 24 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 12 sheets defined 54.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 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: 1.77 Time building geometry restraints manager: 1.58 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: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.240 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.620 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.18), residues: 1763 helix: -1.25 (0.15), residues: 855 sheet: -0.69 (0.40), residues: 162 loop : -0.13 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG C 62 TYR 0.189 0.022 TYR F 132 PHE 0.097 0.015 PHE A 24 TRP 0.088 0.024 TRP F 433 HIS 0.016 0.004 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.01589 (14218) covalent geometry : angle 1.96167 (19332) SS BOND : bond 0.01324 ( 1) SS BOND : angle 3.72086 ( 2) hydrogen bonds : bond 0.17024 ( 703) hydrogen bonds : angle 7.80604 ( 2061) metal coordination : bond 0.09776 ( 8) metal coordination : angle 7.44358 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7285 (tpp) cc_final: 0.7000 (tpt) REVERT: A 151 MET cc_start: 0.6573 (mtp) cc_final: 0.6263 (mtp) REVERT: A 197 ASN cc_start: 0.7801 (t0) cc_final: 0.7198 (m-40) REVERT: A 200 ASP cc_start: 0.6644 (t70) cc_final: 0.6166 (t0) REVERT: A 205 MET cc_start: 0.7374 (tpp) cc_final: 0.6902 (mmm) REVERT: A 223 MET cc_start: 0.7614 (tpp) cc_final: 0.7317 (tpt) REVERT: A 228 MET cc_start: 0.6819 (mmm) cc_final: 0.6574 (mmt) REVERT: A 246 THR cc_start: 0.7366 (t) cc_final: 0.7132 (p) REVERT: A 247 ARG cc_start: 0.6669 (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: 0.6974 (mtp) REVERT: B 205 ARG cc_start: 0.7186 (ttm-80) cc_final: 0.6778 (ttt-90) REVERT: B 207 MET cc_start: 0.7495 (ptt) cc_final: 0.7280 (ptt) REVERT: B 224 SER cc_start: 0.7726 (m) cc_final: 0.7176 (p) REVERT: B 254 MET cc_start: 0.7660 (ptm) cc_final: 0.7401 (ptp) REVERT: C 24 ASP cc_start: 0.7924 (t0) cc_final: 0.7641 (t0) REVERT: C 26 ILE cc_start: 0.7092 (mm) cc_final: 0.6857 (mm) REVERT: C 32 GLN cc_start: 0.7315 (mp10) cc_final: 0.7023 (mp10) REVERT: C 46 LYS cc_start: 0.6380 (mtmt) cc_final: 0.6083 (mtpt) REVERT: C 53 ILE cc_start: 0.7933 (pt) cc_final: 0.7589 (mp) REVERT: C 67 LYS cc_start: 0.7425 (mtmm) cc_final: 0.6841 (mtmm) REVERT: C 73 GLN cc_start: 0.6530 (mp-120) cc_final: 0.6142 (mp-120) REVERT: C 90 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6885 (mt-10) REVERT: C 97 ASP cc_start: 0.6894 (t0) cc_final: 0.6678 (t0) REVERT: C 106 TYR cc_start: 0.8126 (m-80) cc_final: 0.7653 (m-80) REVERT: C 117 LYS cc_start: 0.7284 (ttpt) cc_final: 0.6961 (ttpt) REVERT: C 120 GLN cc_start: 0.7986 (mt0) cc_final: 0.7785 (mt0) REVERT: C 173 LYS cc_start: 0.7229 (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: 0.7955 (tt0) REVERT: D 243 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7393 (ttpp) REVERT: D 247 ASP cc_start: 0.6827 (p0) cc_final: 0.6584 (p0) REVERT: D 251 ASN cc_start: 0.7893 (m110) cc_final: 0.7500 (m-40) REVERT: D 300 ARG cc_start: 0.7580 (ptt-90) cc_final: 0.7232 (ptt-90) REVERT: D 312 GLN cc_start: 0.7345 (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: 0.6869 (mmm) REVERT: F 156 LYS cc_start: 0.7643 (mtmm) cc_final: 0.7352 (mtpp) REVERT: F 169 ARG cc_start: 0.7012 (ptt-90) cc_final: 0.6617 (ptt90) REVERT: F 180 MET cc_start: 0.7437 (mtp) cc_final: 0.7045 (mtm) REVERT: F 195 MET cc_start: 0.7249 (tpt) cc_final: 0.6763 (tpt) REVERT: F 201 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6250 (mm-30) REVERT: F 273 ILE cc_start: 0.6760 (mt) cc_final: 0.6423 (mm) REVERT: F 280 LYS cc_start: 0.7747 (mmtm) cc_final: 0.7472 (mmmm) REVERT: F 286 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7147 (mt-10) REVERT: F 306 ASP cc_start: 0.6438 (t0) cc_final: 0.6229 (m-30) REVERT: F 328 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7666 (mp10) REVERT: F 342 MET cc_start: 0.8102 (ttm) cc_final: 0.7863 (ttp) REVERT: F 357 GLU cc_start: 0.6278 (mp0) cc_final: 0.6039 (mp0) REVERT: F 364 LYS cc_start: 0.7649 (ttpp) cc_final: 0.7327 (tttp) REVERT: F 395 MET cc_start: 0.7147 (mtm) cc_final: 0.6917 (mtp) REVERT: F 406 GLN cc_start: 0.7798 (mt0) cc_final: 0.7491 (mt0) REVERT: F 416 GLU cc_start: 0.7033 (tt0) cc_final: 0.6454 (tp30) REVERT: F 419 LYS cc_start: 0.7174 (tttp) cc_final: 0.6726 (ttpp) REVERT: F 420 ARG cc_start: 0.7258 (mtt-85) cc_final: 0.6863 (mtp85) REVERT: F 423 ASP cc_start: 0.7133 (t0) cc_final: 0.6700 (t0) REVERT: F 430 MET cc_start: 0.7605 (tpp) cc_final: 0.7181 (mmm) REVERT: F 449 SER cc_start: 0.7491 (p) cc_final: 0.7030 (m) REVERT: F 461 LYS cc_start: 0.7343 (mmtt) cc_final: 0.7063 (mptt) REVERT: F 485 GLU cc_start: 0.6828 (tt0) cc_final: 0.6608 (tt0) REVERT: F 489 GLN cc_start: 0.6763 (mm-40) cc_final: 0.6505 (mm-40) REVERT: F 515 GLU cc_start: 0.7196 (tt0) cc_final: 0.6983 (tt0) REVERT: F 530 GLU cc_start: 0.7523 (pm20) cc_final: 0.7245 (pm20) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.6594 time to fit residues: 323.0136 Evaluate side-chains 401 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0970 overall best weight: 0.2378 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118322 restraints weight = 17644.692| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.44 r_work: 0.3504 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14227 Z= 0.143 Angle : 0.656 14.460 19358 Z= 0.331 Chirality : 0.046 0.245 2181 Planarity : 0.005 0.048 2477 Dihedral : 7.732 150.890 1960 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.75 % Allowed : 10.72 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.20), residues: 1763 helix: 0.46 (0.17), residues: 868 sheet: -0.57 (0.38), residues: 175 loop : 0.28 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 298 TYR 0.020 0.002 TYR B 25 PHE 0.025 0.002 PHE F 107 TRP 0.021 0.002 TRP A 293 HIS 0.007 0.001 HIS C 119 Details of bonding type rmsd covalent geometry : bond 0.00312 (14218) covalent geometry : angle 0.62154 (19332) SS BOND : bond 0.00158 ( 1) SS BOND : angle 2.69430 ( 2) hydrogen bonds : bond 0.04489 ( 703) hydrogen bonds : angle 5.41623 ( 2061) metal coordination : bond 0.01226 ( 8) metal coordination : angle 5.93575 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 376 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7977 (mt) REVERT: A 56 LEU cc_start: 0.8276 (mt) cc_final: 0.8027 (mp) REVERT: A 205 MET cc_start: 0.8052 (tpp) cc_final: 0.7798 (mmm) REVERT: A 223 MET cc_start: 0.8243 (tpp) cc_final: 0.7886 (tpt) REVERT: B 205 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7570 (ttt90) REVERT: C 34 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7167 (tt0) REVERT: C 44 SER cc_start: 0.7546 (m) cc_final: 0.7320 (p) REVERT: C 117 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7686 (ttpt) REVERT: C 179 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: C 203 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7461 (mt-10) REVERT: C 227 MET cc_start: 0.8089 (ttm) cc_final: 0.7867 (mtt) REVERT: D 49 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8336 (mttp) REVERT: D 73 MET cc_start: 0.8001 (mmt) cc_final: 0.7801 (mmt) REVERT: D 133 SER cc_start: 0.7515 (OUTLIER) cc_final: 0.7262 (p) REVERT: D 195 SER cc_start: 0.7875 (t) cc_final: 0.7638 (m) REVERT: D 312 GLN cc_start: 0.7730 (mt0) cc_final: 0.7500 (mt0) REVERT: F 54 ASP cc_start: 0.7605 (m-30) cc_final: 0.7393 (m-30) REVERT: F 100 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7970 (ptpp) REVERT: F 106 GLU cc_start: 0.6846 (pt0) cc_final: 0.6559 (pt0) REVERT: F 129 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7581 (mp-120) REVERT: F 146 MET cc_start: 0.7890 (mmm) cc_final: 0.7535 (mmm) REVERT: F 180 MET cc_start: 0.8070 (mtp) cc_final: 0.7869 (mtm) REVERT: F 342 MET cc_start: 0.8428 (ttm) cc_final: 0.8152 (ttp) REVERT: F 357 GLU cc_start: 0.7075 (mp0) cc_final: 0.6851 (mp0) outliers start: 26 outliers final: 11 residues processed: 380 average time/residue: 0.6723 time to fit residues: 275.9742 Evaluate side-chains 350 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 334 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 338 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 108 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 0.0000 chunk 17 optimal weight: 0.6980 chunk 158 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 D 21 HIS D 129 ASN D 208 GLN F 206 ASN F 472 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.125304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115545 restraints weight = 17953.370| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.54 r_work: 0.3472 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14227 Z= 0.197 Angle : 0.660 17.012 19358 Z= 0.322 Chirality : 0.047 0.245 2181 Planarity : 0.005 0.057 2477 Dihedral : 7.231 134.192 1960 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.57 % Allowed : 14.09 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.20), residues: 1763 helix: 0.62 (0.17), residues: 871 sheet: -0.72 (0.36), residues: 188 loop : 0.28 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 47 TYR 0.017 0.002 TYR B 25 PHE 0.024 0.002 PHE B 283 TRP 0.020 0.002 TRP A 293 HIS 0.006 0.001 HIS C 119 Details of bonding type rmsd covalent geometry : bond 0.00484 (14218) covalent geometry : angle 0.61982 (19332) SS BOND : bond 0.00444 ( 1) SS BOND : angle 2.05522 ( 2) hydrogen bonds : bond 0.04357 ( 703) hydrogen bonds : angle 5.17199 ( 2061) metal coordination : bond 0.01222 ( 8) metal coordination : angle 6.42946 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 360 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8251 (mt) cc_final: 0.7923 (mt) REVERT: A 56 LEU cc_start: 0.8274 (mt) cc_final: 0.8042 (mp) REVERT: A 223 MET cc_start: 0.8349 (tpp) cc_final: 0.8053 (tpt) REVERT: A 247 ARG cc_start: 0.7405 (mmm160) cc_final: 0.7134 (mmm160) REVERT: A 325 ASP cc_start: 0.7826 (t0) cc_final: 0.7611 (m-30) REVERT: B 22 PHE cc_start: 0.7869 (t80) cc_final: 0.7593 (t80) REVERT: B 205 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7515 (ttt90) REVERT: B 228 SER cc_start: 0.7884 (t) cc_final: 0.7612 (p) REVERT: C 66 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 101 SER cc_start: 0.7816 (t) cc_final: 0.7588 (p) REVERT: C 117 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7666 (ttpt) REVERT: C 173 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7629 (mtpp) REVERT: C 203 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 212 HIS cc_start: 0.7932 (m-70) cc_final: 0.7720 (m90) REVERT: C 227 MET cc_start: 0.8314 (ttm) cc_final: 0.8086 (mtt) REVERT: D 249 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7820 (mt) REVERT: D 285 SER cc_start: 0.8115 (t) cc_final: 0.7820 (p) REVERT: D 300 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7366 (ptt-90) REVERT: D 312 GLN cc_start: 0.7820 (mt0) cc_final: 0.7586 (mt0) REVERT: F 54 ASP cc_start: 0.7688 (m-30) cc_final: 0.7441 (m-30) REVERT: F 129 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7713 (mp-120) REVERT: F 202 LYS cc_start: 0.7770 (mttt) cc_final: 0.7495 (mtpt) REVERT: F 357 GLU cc_start: 0.7108 (mp0) cc_final: 0.6851 (mp0) REVERT: F 449 SER cc_start: 0.7683 (t) cc_final: 0.7383 (m) REVERT: F 475 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8159 (ttm170) REVERT: F 496 ASP cc_start: 0.7900 (t0) cc_final: 0.7687 (t70) outliers start: 53 outliers final: 17 residues processed: 373 average time/residue: 0.7055 time to fit residues: 285.4047 Evaluate side-chains 368 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 349 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 300 ARG Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 238 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 120 optimal weight: 0.0970 chunk 51 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 79 HIS B 210 ASN C 120 GLN C 179 GLN C 189 GLN C 212 HIS D 187 GLN D 252 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115519 restraints weight = 17803.934| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.45 r_work: 0.3483 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14227 Z= 0.195 Angle : 0.644 18.240 19358 Z= 0.313 Chirality : 0.046 0.257 2181 Planarity : 0.005 0.059 2477 Dihedral : 7.002 125.904 1960 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.98 % Allowed : 15.31 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.20), residues: 1763 helix: 0.68 (0.17), residues: 870 sheet: -0.70 (0.37), residues: 183 loop : 0.18 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 255 TYR 0.018 0.002 TYR C 317 PHE 0.020 0.002 PHE F 107 TRP 0.017 0.002 TRP A 293 HIS 0.005 0.001 HIS C 119 Details of bonding type rmsd covalent geometry : bond 0.00475 (14218) covalent geometry : angle 0.60440 (19332) SS BOND : bond 0.00410 ( 1) SS BOND : angle 1.87210 ( 2) hydrogen bonds : bond 0.04148 ( 703) hydrogen bonds : angle 5.10917 ( 2061) metal coordination : bond 0.01038 ( 8) metal coordination : angle 6.34929 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 383 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8322 (mt) cc_final: 0.7961 (mt) REVERT: A 56 LEU cc_start: 0.8312 (mt) cc_final: 0.8088 (mp) REVERT: A 223 MET cc_start: 0.8328 (tpp) cc_final: 0.8102 (tpt) REVERT: A 247 ARG cc_start: 0.7283 (mmm160) cc_final: 0.7063 (mmm160) REVERT: B 62 ARG cc_start: 0.8452 (mmt90) cc_final: 0.8146 (mpt-90) REVERT: B 205 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7510 (ttt90) REVERT: B 228 SER cc_start: 0.7910 (t) cc_final: 0.7659 (p) REVERT: C 66 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 101 SER cc_start: 0.7757 (t) cc_final: 0.7557 (p) REVERT: C 117 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7693 (ttpt) REVERT: C 173 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7714 (mtpp) REVERT: C 203 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7430 (mt-10) REVERT: C 241 ILE cc_start: 0.8382 (mm) cc_final: 0.8124 (tt) REVERT: D 33 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7258 (ttp80) REVERT: D 195 SER cc_start: 0.7906 (t) cc_final: 0.7681 (m) REVERT: D 249 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7857 (mt) REVERT: D 300 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7291 (ptt-90) REVERT: F 54 ASP cc_start: 0.7701 (m-30) cc_final: 0.7488 (m-30) REVERT: F 86 GLU cc_start: 0.7588 (mp0) cc_final: 0.7286 (mp0) REVERT: F 129 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7668 (mp-120) REVERT: F 146 MET cc_start: 0.7963 (mmm) cc_final: 0.7674 (mmm) REVERT: F 357 GLU cc_start: 0.7099 (mp0) cc_final: 0.6863 (mp0) REVERT: F 360 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8264 (mtpt) REVERT: F 430 MET cc_start: 0.8053 (mmm) cc_final: 0.7804 (mmm) REVERT: F 449 SER cc_start: 0.7628 (t) cc_final: 0.7367 (m) REVERT: F 475 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8128 (ttm170) REVERT: F 496 ASP cc_start: 0.7903 (t0) cc_final: 0.7701 (t70) outliers start: 59 outliers final: 24 residues processed: 395 average time/residue: 0.6992 time to fit residues: 299.4408 Evaluate side-chains 404 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 376 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 26 ILE 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 33 ARG Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 300 ARG Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 360 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 152 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 149 optimal weight: 0.0270 chunk 162 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 164 optimal weight: 0.3980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 179 GLN C 201 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN F 114 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116164 restraints weight = 17947.694| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.50 r_work: 0.3483 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14227 Z= 0.163 Angle : 0.620 17.781 19358 Z= 0.299 Chirality : 0.045 0.269 2181 Planarity : 0.005 0.055 2477 Dihedral : 6.828 122.676 1960 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.71 % Allowed : 17.40 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.20), residues: 1763 helix: 0.78 (0.17), residues: 870 sheet: -0.71 (0.38), residues: 184 loop : 0.22 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 255 TYR 0.017 0.002 TYR C 317 PHE 0.031 0.002 PHE F 107 TRP 0.015 0.001 TRP A 293 HIS 0.005 0.001 HIS F 426 Details of bonding type rmsd covalent geometry : bond 0.00394 (14218) covalent geometry : angle 0.57960 (19332) SS BOND : bond 0.00307 ( 1) SS BOND : angle 1.65186 ( 2) hydrogen bonds : bond 0.03905 ( 703) hydrogen bonds : angle 5.01569 ( 2061) metal coordination : bond 0.00919 ( 8) metal coordination : angle 6.28915 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 387 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8257 (mt) cc_final: 0.8047 (mp) REVERT: A 223 MET cc_start: 0.8337 (tpp) cc_final: 0.8103 (tpt) REVERT: A 247 ARG cc_start: 0.7456 (mmm160) cc_final: 0.7250 (mmm160) REVERT: A 271 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7891 (p) REVERT: B 62 ARG cc_start: 0.8446 (mmt90) cc_final: 0.8017 (mpt180) REVERT: B 205 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7504 (ttt90) REVERT: B 228 SER cc_start: 0.7890 (t) cc_final: 0.7645 (p) REVERT: C 66 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 101 SER cc_start: 0.7754 (t) cc_final: 0.7542 (p) REVERT: C 117 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7671 (ttpt) REVERT: C 203 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7429 (mt-10) REVERT: C 241 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8066 (tt) REVERT: D 33 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7190 (ttp80) REVERT: D 195 SER cc_start: 0.7908 (t) cc_final: 0.7707 (m) REVERT: D 249 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7875 (mt) REVERT: D 300 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7305 (ptt-90) REVERT: D 312 GLN cc_start: 0.7723 (mt0) cc_final: 0.7477 (mm-40) REVERT: F 54 ASP cc_start: 0.7745 (m-30) cc_final: 0.7526 (m-30) REVERT: F 86 GLU cc_start: 0.7585 (mp0) cc_final: 0.7252 (mp0) REVERT: F 129 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7725 (mp-120) REVERT: F 350 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7784 (mm110) REVERT: F 357 GLU cc_start: 0.7109 (mp0) cc_final: 0.6875 (mp0) REVERT: F 449 SER cc_start: 0.7579 (t) cc_final: 0.7331 (m) REVERT: F 475 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8188 (ttm170) outliers start: 55 outliers final: 24 residues processed: 400 average time/residue: 0.6713 time to fit residues: 290.9152 Evaluate side-chains 408 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 379 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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 26 ILE 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 241 ILE 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 96 LEU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 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 230 ASP Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 338 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 214 ASN C 120 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 201 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115647 restraints weight = 17744.464| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.48 r_work: 0.3474 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14227 Z= 0.188 Angle : 0.636 18.470 19358 Z= 0.306 Chirality : 0.045 0.255 2181 Planarity : 0.005 0.083 2477 Dihedral : 6.806 121.679 1960 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.30 % Allowed : 18.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.20), residues: 1763 helix: 0.83 (0.17), residues: 869 sheet: -0.63 (0.38), residues: 184 loop : 0.19 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 255 TYR 0.022 0.002 TYR F 140 PHE 0.032 0.002 PHE F 107 TRP 0.014 0.001 TRP A 293 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00459 (14218) covalent geometry : angle 0.59502 (19332) SS BOND : bond 0.00374 ( 1) SS BOND : angle 1.53639 ( 2) hydrogen bonds : bond 0.03946 ( 703) hydrogen bonds : angle 5.01440 ( 2061) metal coordination : bond 0.01061 ( 8) metal coordination : angle 6.42111 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 383 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8312 (mt) cc_final: 0.8089 (mp) REVERT: A 223 MET cc_start: 0.8353 (tpp) cc_final: 0.8044 (tpt) REVERT: A 247 ARG cc_start: 0.7534 (mmm160) cc_final: 0.7302 (mmm160) REVERT: B 59 GLU cc_start: 0.7170 (tt0) cc_final: 0.6946 (tt0) REVERT: B 62 ARG cc_start: 0.8451 (mmt90) cc_final: 0.8015 (mpt180) REVERT: B 205 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7487 (ttt90) REVERT: B 228 SER cc_start: 0.7920 (t) cc_final: 0.7678 (p) REVERT: C 66 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7688 (mt-10) REVERT: C 117 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7667 (ttpt) REVERT: C 129 GLN cc_start: 0.7848 (tp40) cc_final: 0.7579 (tp40) REVERT: C 203 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7426 (mt-10) REVERT: C 241 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8063 (tt) REVERT: D 33 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7488 (mtp85) REVERT: D 36 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7885 (mppt) REVERT: D 195 SER cc_start: 0.7840 (t) cc_final: 0.7625 (m) REVERT: D 249 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7885 (mt) REVERT: D 312 GLN cc_start: 0.7745 (mt0) cc_final: 0.7504 (mm-40) REVERT: F 54 ASP cc_start: 0.7730 (m-30) cc_final: 0.7510 (m-30) REVERT: F 86 GLU cc_start: 0.7548 (mp0) cc_final: 0.7203 (mp0) REVERT: F 129 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7748 (mp-120) REVERT: F 357 GLU cc_start: 0.7127 (mp0) cc_final: 0.6799 (mp0) REVERT: F 416 GLU cc_start: 0.7406 (tp30) cc_final: 0.7092 (tm-30) REVERT: F 420 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7216 (mtt90) REVERT: F 449 SER cc_start: 0.7579 (t) cc_final: 0.7327 (m) REVERT: F 475 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8187 (ttm170) outliers start: 49 outliers final: 28 residues processed: 402 average time/residue: 0.6832 time to fit residues: 297.7017 Evaluate side-chains 412 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 380 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 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 67 LYS Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 99 MET 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 69 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 279 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 44 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN F 114 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115524 restraints weight = 17853.073| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.45 r_work: 0.3486 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14227 Z= 0.170 Angle : 0.631 18.204 19358 Z= 0.303 Chirality : 0.045 0.259 2181 Planarity : 0.005 0.047 2477 Dihedral : 6.713 120.057 1960 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.57 % Allowed : 19.55 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.20), residues: 1763 helix: 0.91 (0.18), residues: 869 sheet: -0.60 (0.38), residues: 184 loop : 0.21 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 255 TYR 0.019 0.002 TYR C 317 PHE 0.033 0.002 PHE F 107 TRP 0.014 0.001 TRP A 293 HIS 0.004 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00413 (14218) covalent geometry : angle 0.59019 (19332) SS BOND : bond 0.00335 ( 1) SS BOND : angle 1.47008 ( 2) hydrogen bonds : bond 0.03862 ( 703) hydrogen bonds : angle 4.96570 ( 2061) metal coordination : bond 0.00965 ( 8) metal coordination : angle 6.38081 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 372 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8278 (mt) cc_final: 0.8056 (mp) REVERT: A 223 MET cc_start: 0.8364 (tpp) cc_final: 0.8049 (tpt) REVERT: A 247 ARG cc_start: 0.7503 (mmm160) cc_final: 0.7272 (mmm160) REVERT: A 271 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7897 (p) REVERT: B 59 GLU cc_start: 0.7175 (tt0) cc_final: 0.6939 (tt0) REVERT: B 205 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7452 (ttt90) REVERT: B 228 SER cc_start: 0.7899 (t) cc_final: 0.7662 (p) REVERT: C 66 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7678 (mt-10) REVERT: C 117 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7655 (ttpt) REVERT: C 129 GLN cc_start: 0.7828 (tp40) cc_final: 0.7408 (tp-100) REVERT: C 173 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7713 (mtpp) REVERT: C 203 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7388 (mt-10) REVERT: C 241 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8005 (tt) REVERT: D 33 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7446 (mtp85) REVERT: D 176 LEU cc_start: 0.8950 (mt) cc_final: 0.8732 (mt) REVERT: D 249 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7884 (mt) REVERT: D 312 GLN cc_start: 0.7754 (mt0) cc_final: 0.7531 (mm-40) REVERT: F 54 ASP cc_start: 0.7750 (m-30) cc_final: 0.7538 (m-30) REVERT: F 86 GLU cc_start: 0.7539 (mp0) cc_final: 0.7188 (mp0) REVERT: F 129 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7736 (mp-120) REVERT: F 241 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7744 (m) REVERT: F 357 GLU cc_start: 0.7130 (mp0) cc_final: 0.6757 (mp0) REVERT: F 449 SER cc_start: 0.7548 (t) cc_final: 0.7293 (m) REVERT: F 475 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8200 (ttm170) outliers start: 53 outliers final: 22 residues processed: 390 average time/residue: 0.6741 time to fit residues: 285.1047 Evaluate side-chains 401 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 374 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 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 182 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain F residue 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 501 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 201 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN F 114 ASN F 388 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.115141 restraints weight = 17785.407| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.52 r_work: 0.3473 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14227 Z= 0.197 Angle : 0.651 18.728 19358 Z= 0.312 Chirality : 0.046 0.257 2181 Planarity : 0.005 0.081 2477 Dihedral : 6.725 120.217 1960 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.30 % Allowed : 20.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.20), residues: 1763 helix: 0.86 (0.17), residues: 868 sheet: -0.61 (0.38), residues: 184 loop : 0.17 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 255 TYR 0.023 0.002 TYR F 140 PHE 0.035 0.002 PHE F 107 TRP 0.013 0.001 TRP A 293 HIS 0.005 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00484 (14218) covalent geometry : angle 0.61068 (19332) SS BOND : bond 0.00437 ( 1) SS BOND : angle 1.43098 ( 2) hydrogen bonds : bond 0.03985 ( 703) hydrogen bonds : angle 4.97489 ( 2061) metal coordination : bond 0.01122 ( 8) metal coordination : angle 6.46394 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 365 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8307 (mt) cc_final: 0.8072 (mp) REVERT: A 223 MET cc_start: 0.8370 (tpp) cc_final: 0.8071 (tpt) REVERT: A 247 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7341 (mmm160) REVERT: B 59 GLU cc_start: 0.7260 (tt0) cc_final: 0.7008 (tt0) REVERT: B 205 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7455 (ttt90) REVERT: B 228 SER cc_start: 0.7940 (t) cc_final: 0.7684 (p) REVERT: B 234 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7283 (tpt) REVERT: C 66 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7721 (mt-10) REVERT: C 117 LYS cc_start: 0.7973 (ttpt) cc_final: 0.7671 (ttpt) REVERT: C 173 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7757 (mtpp) REVERT: C 179 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7192 (mt0) REVERT: C 203 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7414 (mt-10) REVERT: C 241 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8018 (tt) REVERT: D 33 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7467 (mtp85) REVERT: D 61 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7971 (mppt) REVERT: D 176 LEU cc_start: 0.8944 (mt) cc_final: 0.8720 (mt) REVERT: D 249 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7907 (mt) REVERT: D 298 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7282 (ptm160) REVERT: F 54 ASP cc_start: 0.7740 (m-30) cc_final: 0.7528 (m-30) REVERT: F 86 GLU cc_start: 0.7604 (mp0) cc_final: 0.7246 (mp0) REVERT: F 129 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7758 (mp-120) REVERT: F 241 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7749 (m) REVERT: F 357 GLU cc_start: 0.7189 (mp0) cc_final: 0.6894 (mp0) REVERT: F 449 SER cc_start: 0.7559 (t) cc_final: 0.7307 (m) outliers start: 49 outliers final: 31 residues processed: 380 average time/residue: 0.6876 time to fit residues: 283.0785 Evaluate side-chains 412 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 373 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 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 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 234 MET 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 134 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 211 THR 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 61 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 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 364 LYS Chi-restraints excluded: chain F residue 419 LYS Chi-restraints excluded: chain F residue 501 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 145 optimal weight: 0.8980 chunk 130 optimal weight: 0.0670 chunk 65 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 149 optimal weight: 0.9990 chunk 93 optimal weight: 0.0020 chunk 127 optimal weight: 0.6980 overall best weight: 0.2484 ------------------------------------------------------------------------------- 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 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 = 0.3720 r_free = 0.3720 target = 0.126920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117259 restraints weight = 17573.277| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.51 r_work: 0.3496 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14227 Z= 0.126 Angle : 0.615 16.534 19358 Z= 0.294 Chirality : 0.043 0.160 2181 Planarity : 0.005 0.049 2477 Dihedral : 6.575 118.947 1960 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.36 % Allowed : 21.58 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.20), residues: 1763 helix: 1.06 (0.18), residues: 864 sheet: -0.53 (0.39), residues: 180 loop : 0.25 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 255 TYR 0.017 0.002 TYR C 317 PHE 0.036 0.001 PHE F 107 TRP 0.015 0.001 TRP A 293 HIS 0.005 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00294 (14218) covalent geometry : angle 0.57537 (19332) SS BOND : bond 0.00194 ( 1) SS BOND : angle 1.36155 ( 2) hydrogen bonds : bond 0.03615 ( 703) hydrogen bonds : angle 4.86842 ( 2061) metal coordination : bond 0.00697 ( 8) metal coordination : angle 6.15899 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 379 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8250 (mt) cc_final: 0.8041 (mp) REVERT: A 223 MET cc_start: 0.8370 (tpp) cc_final: 0.8015 (tpt) REVERT: A 247 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7324 (mmm160) REVERT: B 59 GLU cc_start: 0.7244 (tt0) cc_final: 0.6989 (tt0) REVERT: B 205 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7439 (ttt90) REVERT: B 228 SER cc_start: 0.7875 (t) cc_final: 0.7625 (p) REVERT: C 66 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 117 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7622 (ttpt) REVERT: C 153 GLN cc_start: 0.7993 (mt0) cc_final: 0.7712 (mt0) REVERT: C 163 MET cc_start: 0.8285 (mtm) cc_final: 0.8008 (mtt) REVERT: C 203 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7351 (mt-10) REVERT: C 241 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7939 (tt) REVERT: C 255 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7567 (ttm170) REVERT: D 33 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7462 (mtp85) REVERT: D 176 LEU cc_start: 0.8901 (mt) cc_final: 0.8674 (mt) REVERT: D 249 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7881 (mt) REVERT: D 298 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7366 (ptm160) REVERT: D 312 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7647 (mm-40) REVERT: F 86 GLU cc_start: 0.7563 (mp0) cc_final: 0.7216 (mp0) REVERT: F 129 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7752 (mp-120) REVERT: F 180 MET cc_start: 0.8111 (mtp) cc_final: 0.7891 (mtm) REVERT: F 241 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7728 (m) REVERT: F 357 GLU cc_start: 0.7170 (mp0) cc_final: 0.6878 (mp0) REVERT: F 449 SER cc_start: 0.7490 (t) cc_final: 0.7262 (m) outliers start: 35 outliers final: 19 residues processed: 388 average time/residue: 0.7007 time to fit residues: 294.3158 Evaluate side-chains 393 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 368 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 119 VAL 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 96 GLN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 211 THR 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 69 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 298 ARG Chi-restraints excluded: chain D residue 312 GLN 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 137 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 136 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 87 optimal weight: 0.0020 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 137 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 201 GLN C 251 GLN D 187 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116909 restraints weight = 17754.809| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.44 r_work: 0.3496 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14227 Z= 0.161 Angle : 0.638 17.022 19358 Z= 0.306 Chirality : 0.044 0.173 2181 Planarity : 0.005 0.047 2477 Dihedral : 6.592 119.146 1960 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.29 % Allowed : 21.92 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.20), residues: 1763 helix: 1.08 (0.18), residues: 862 sheet: -0.53 (0.39), residues: 180 loop : 0.22 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 255 TYR 0.024 0.002 TYR F 140 PHE 0.038 0.002 PHE F 107 TRP 0.013 0.001 TRP A 293 HIS 0.006 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00390 (14218) covalent geometry : angle 0.60093 (19332) SS BOND : bond 0.00351 ( 1) SS BOND : angle 1.35245 ( 2) hydrogen bonds : bond 0.03756 ( 703) hydrogen bonds : angle 4.89733 ( 2061) metal coordination : bond 0.00928 ( 8) metal coordination : angle 6.12985 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 370 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8268 (mt) cc_final: 0.8053 (mp) REVERT: A 223 MET cc_start: 0.8340 (tpp) cc_final: 0.8004 (tpt) REVERT: A 247 ARG cc_start: 0.7487 (mmm160) cc_final: 0.7219 (mmm160) REVERT: B 59 GLU cc_start: 0.7234 (tt0) cc_final: 0.7002 (tt0) REVERT: B 205 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7437 (ttt90) REVERT: B 228 SER cc_start: 0.7914 (t) cc_final: 0.7670 (p) REVERT: C 66 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7689 (mt-10) REVERT: C 117 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7576 (ttpt) REVERT: C 163 MET cc_start: 0.8300 (mtm) cc_final: 0.8017 (mtt) REVERT: C 173 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7731 (mtpp) REVERT: C 203 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7379 (mt-10) REVERT: C 241 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7886 (tt) REVERT: D 25 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7872 (mtpm) REVERT: D 33 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7493 (mtp85) REVERT: D 176 LEU cc_start: 0.8916 (mt) cc_final: 0.8686 (mt) REVERT: D 249 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7888 (mt) REVERT: D 298 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7405 (ptm160) REVERT: F 86 GLU cc_start: 0.7513 (mp0) cc_final: 0.7178 (mp0) REVERT: F 129 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7765 (mp-120) REVERT: F 146 MET cc_start: 0.8105 (mtp) cc_final: 0.7679 (mtm) REVERT: F 180 MET cc_start: 0.8121 (mtp) cc_final: 0.7864 (mtm) REVERT: F 241 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7722 (m) REVERT: F 357 GLU cc_start: 0.7194 (mp0) cc_final: 0.6843 (mp0) REVERT: F 449 SER cc_start: 0.7491 (t) cc_final: 0.7283 (m) outliers start: 34 outliers final: 22 residues processed: 378 average time/residue: 0.7203 time to fit residues: 295.1680 Evaluate side-chains 403 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 375 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 119 VAL 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 283 PHE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 64 MET 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 C residue 241 ILE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 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 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 129 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 126 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 531 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.126225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117032 restraints weight = 17634.471| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.43 r_work: 0.3496 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3420 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= 0.166 Angle : 0.644 17.395 19358 Z= 0.308 Chirality : 0.045 0.173 2181 Planarity : 0.005 0.108 2477 Dihedral : 6.593 118.588 1960 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.09 % Allowed : 21.98 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.20), residues: 1763 helix: 1.10 (0.18), residues: 862 sheet: -0.57 (0.38), residues: 190 loop : 0.23 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 255 TYR 0.025 0.002 TYR F 354 PHE 0.039 0.002 PHE F 107 TRP 0.013 0.001 TRP A 293 HIS 0.006 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00403 (14218) covalent geometry : angle 0.60725 (19332) SS BOND : bond 0.00368 ( 1) SS BOND : angle 1.31517 ( 2) hydrogen bonds : bond 0.03780 ( 703) hydrogen bonds : angle 4.89345 ( 2061) metal coordination : bond 0.00948 ( 8) metal coordination : angle 6.13119 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6204.42 seconds wall clock time: 106 minutes 12.11 seconds (6372.11 seconds total)