Starting phenix.real_space_refine on Thu Jun 19 11:16:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fs6_29415/06_2025/8fs6_29415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs6_29415/06_2025/8fs6_29415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fs6_29415/06_2025/8fs6_29415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs6_29415/06_2025/8fs6_29415.map" model { file = "/net/cci-nas-00/data/ceres_data/8fs6_29415/06_2025/8fs6_29415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs6_29415/06_2025/8fs6_29415.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 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 P 71 5.49 5 Mg 4 5.21 5 S 115 5.16 5 C 13899 2.51 5 N 3821 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22246 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3559 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2743 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "F" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2238 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 9, 'TRANS': 267} Chain breaks: 6 Chain: "G" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2366 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain breaks: 1 Chain: "H" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2314 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 4 Chain: "I" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "J" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 313 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.28, per 1000 atoms: 0.64 Number of scatterers: 22246 At special positions: 0 Unit cell: (115.092, 127.512, 138.276, 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) S 115 16.00 P 71 15.00 Mg 4 11.99 O 4336 8.00 N 3821 7.00 C 13899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 2.6 seconds 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5016 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 16 sheets defined 50.7% alpha, 16.6% beta 22 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 7.62 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 118 through 131 removed outlier: 4.299A pdb=" N LYS A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 194 through 210 removed outlier: 3.846A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.518A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.768A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.743A pdb=" N ILE A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.895A pdb=" N CYS A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.919A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.604A pdb=" N ARG A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 470 removed outlier: 3.569A pdb=" N LYS A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 removed outlier: 3.704A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.682A pdb=" N VAL B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.990A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.841A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.813A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 244 through 257 removed outlier: 3.786A pdb=" N GLN B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 251 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.519A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.693A pdb=" N LEU C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.676A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 44 removed outlier: 3.844A pdb=" N LYS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 3.526A pdb=" N VAL C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 96 through 103 Processing helix chain 'C' and resid 119 through 122 Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 129 through 137 removed outlier: 4.012A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.738A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.572A pdb=" N CYS C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.715A pdb=" N LYS C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.597A pdb=" N SER C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 242 through 254 removed outlier: 3.707A pdb=" N VAL C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 removed outlier: 3.810A pdb=" N TYR C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.575A pdb=" N LYS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.844A pdb=" N ASP C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 335 removed outlier: 3.527A pdb=" N SER C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 45 through 55 removed outlier: 3.716A pdb=" N LEU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.768A pdb=" N ALA D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.077A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.948A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 152 removed outlier: 3.732A pdb=" N ALA D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 removed outlier: 3.671A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.568A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.510A pdb=" N TYR D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 removed outlier: 3.792A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.799A pdb=" N SER D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.569A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.542A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.756A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.535A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.243A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 97 through 104 removed outlier: 6.277A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN E 104 " --> pdb=" O MET E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.906A pdb=" N LEU E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 151 through 161 removed outlier: 4.621A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.725A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.336A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 removed outlier: 3.596A pdb=" N TYR F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR F 25 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 96 through 113 removed outlier: 3.976A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 218 Processing helix chain 'F' and resid 242 through 253 removed outlier: 4.393A pdb=" N VAL F 253 " --> pdb=" O PHE F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 412 through 424 removed outlier: 3.632A pdb=" N ALA F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 27 removed outlier: 3.584A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 86 through 93 Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 244 through 246 No H-bonds generated for 'chain 'G' and resid 244 through 246' Processing helix chain 'G' and resid 247 through 251 removed outlier: 3.681A pdb=" N ILE G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 330 removed outlier: 3.852A pdb=" N THR G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 27 removed outlier: 3.586A pdb=" N VAL H 22 " --> pdb=" O ARG H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 98 through 103 Processing helix chain 'H' and resid 161 through 166 Processing helix chain 'H' and resid 234 through 244 Processing helix chain 'H' and resid 326 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 3.693A pdb=" N GLY A 109 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.206A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.168A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.398A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 69 through 75 removed outlier: 3.523A pdb=" N PHE E 75 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE E 140 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 212 through 213 removed outlier: 7.582A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 79 through 82 removed outlier: 5.058A pdb=" N LEU F 3 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS F 122 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 207 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR F 92 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS F 70 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER F 46 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU F 68 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET F 231 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 408 through 411 removed outlier: 7.568A pdb=" N HIS F 261 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASN F 286 " --> pdb=" O HIS F 261 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG G 129 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER G 127 " --> pdb=" O CYS F 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 62 through 63 removed outlier: 5.819A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 62 through 63 removed outlier: 3.515A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP G 260 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 232 through 238 removed outlier: 3.765A pdb=" N ALA G 193 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE G 202 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.131A pdb=" N PHE G 202 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 78 through 79 Processing sheet with id=AB6, first strand: chain 'H' and resid 78 through 79 removed outlier: 7.209A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN H 365 " --> pdb=" O ASN H 348 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN H 348 " --> pdb=" O GLN H 365 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN H 233 " --> pdb=" O LEU H 293 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU H 293 " --> pdb=" O ASN H 233 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 284 through 288 removed outlier: 3.624A pdb=" N GLU H 251 " --> pdb=" O PHE H 266 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 8.03 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7201 1.36 - 1.51: 6039 1.51 - 1.65: 9331 1.65 - 1.80: 70 1.80 - 1.95: 101 Bond restraints: 22742 Sorted by residual: bond pdb=" C SER E 175 " pdb=" N PRO E 176 " ideal model delta sigma weight residual 1.334 1.365 -0.031 8.40e-03 1.42e+04 1.39e+01 bond pdb=" N ILE F 410 " pdb=" CA ILE F 410 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.18e+01 bond pdb=" N VAL F 267 " pdb=" CA VAL F 267 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N VAL A 148 " pdb=" CA VAL A 148 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N ILE E 96 " pdb=" CA ILE E 96 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.14e-02 7.69e+03 9.39e+00 ... (remaining 22737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 30403 2.28 - 4.56: 511 4.56 - 6.83: 51 6.83 - 9.11: 15 9.11 - 11.39: 4 Bond angle restraints: 30984 Sorted by residual: angle pdb=" N MET F 231 " pdb=" CA MET F 231 " pdb=" C MET F 231 " ideal model delta sigma weight residual 107.61 115.83 -8.22 1.74e+00 3.30e-01 2.23e+01 angle pdb=" N HIS E 18 " pdb=" CA HIS E 18 " pdb=" CB HIS E 18 " ideal model delta sigma weight residual 110.49 118.30 -7.81 1.69e+00 3.50e-01 2.14e+01 angle pdb=" CA SER E 17 " pdb=" C SER E 17 " pdb=" O SER E 17 " ideal model delta sigma weight residual 121.39 116.30 5.09 1.12e+00 7.97e-01 2.06e+01 angle pdb=" CA HIS E 18 " pdb=" CB HIS E 18 " pdb=" CG HIS E 18 " ideal model delta sigma weight residual 113.80 118.22 -4.42 1.00e+00 1.00e+00 1.96e+01 angle pdb=" N ASN E 103 " pdb=" CA ASN E 103 " pdb=" C ASN E 103 " ideal model delta sigma weight residual 113.18 108.05 5.13 1.21e+00 6.83e-01 1.80e+01 ... (remaining 30979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 12470 26.14 - 52.28: 1086 52.28 - 78.42: 183 78.42 - 104.56: 11 104.56 - 130.70: 3 Dihedral angle restraints: 13753 sinusoidal: 6059 harmonic: 7694 Sorted by residual: dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 70.70 -130.70 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 65.75 -125.75 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 58.13 -118.13 1 2.00e+01 2.50e-03 3.53e+01 ... (remaining 13750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3220 0.075 - 0.151: 330 0.151 - 0.226: 30 0.226 - 0.301: 1 0.301 - 0.377: 1 Chirality restraints: 3582 Sorted by residual: chirality pdb=" CG LEU G 327 " pdb=" CB LEU G 327 " pdb=" CD1 LEU G 327 " pdb=" CD2 LEU G 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CG LEU F 5 " pdb=" CB LEU F 5 " pdb=" CD1 LEU F 5 " pdb=" CD2 LEU F 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU B 319 " pdb=" CB LEU B 319 " pdb=" CD1 LEU B 319 " pdb=" CD2 LEU B 319 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3579 not shown) Planarity restraints: 3707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 541 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO A 542 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 542 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 542 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 333 " 0.016 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C ILE H 333 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE H 333 " 0.019 2.00e-02 2.50e+03 pdb=" N THR H 334 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 185 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C CYS E 185 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS E 185 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU E 186 " -0.015 2.00e-02 2.50e+03 ... (remaining 3704 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 245 2.62 - 3.19: 18448 3.19 - 3.76: 35593 3.76 - 4.33: 49813 4.33 - 4.90: 81554 Nonbonded interactions: 185653 Sorted by model distance: nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.045 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.054 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.097 2.170 nonbonded pdb=" OE2 GLU A 187 " pdb="MG MG A 602 " model vdw 2.102 2.170 nonbonded pdb=" O3A AGS A 601 " pdb="MG MG A 602 " model vdw 2.103 2.170 ... (remaining 185648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.170 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: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 55.540 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.004 0.076 22742 Z= 0.237 Angle : 0.676 11.391 30984 Z= 0.403 Chirality : 0.046 0.377 3582 Planarity : 0.004 0.102 3707 Dihedral : 18.463 130.697 8737 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.53 % Allowed : 23.86 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2577 helix: -0.24 (0.15), residues: 1213 sheet: -0.34 (0.23), residues: 542 loop : -0.75 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 352 HIS 0.016 0.001 HIS F 406 PHE 0.030 0.001 PHE E 124 TYR 0.031 0.001 TYR F 466 ARG 0.010 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.19169 ( 1107) hydrogen bonds : angle 7.36545 ( 3197) covalent geometry : bond 0.00373 (22742) covalent geometry : angle 0.67568 (30984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 332 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7001 (mt-10) REVERT: F 79 LEU cc_start: 0.1740 (OUTLIER) cc_final: 0.1391 (mt) REVERT: H 55 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6846 (mtm-85) outliers start: 60 outliers final: 50 residues processed: 326 average time/residue: 1.2369 time to fit residues: 462.6033 Evaluate side-chains 313 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 268 ASN Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 256 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 106 optimal weight: 0.0770 chunk 205 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 237 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 194 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS F 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.187960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136645 restraints weight = 25014.134| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.94 r_work: 0.3362 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22742 Z= 0.122 Angle : 0.521 7.364 30984 Z= 0.279 Chirality : 0.041 0.166 3582 Planarity : 0.004 0.074 3707 Dihedral : 15.947 133.219 3587 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.43 % Allowed : 21.25 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2577 helix: 0.32 (0.15), residues: 1200 sheet: -0.31 (0.22), residues: 554 loop : -0.47 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 69 HIS 0.009 0.001 HIS E 18 PHE 0.016 0.001 PHE F 37 TYR 0.017 0.001 TYR H 166 ARG 0.004 0.000 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 1107) hydrogen bonds : angle 5.09528 ( 3197) covalent geometry : bond 0.00267 (22742) covalent geometry : angle 0.52145 (30984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 284 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8324 (tt) REVERT: A 245 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7701 (t) REVERT: A 372 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.7860 (p) REVERT: C 199 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: C 332 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6750 (mt-10) REVERT: E 164 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7437 (p0) REVERT: E 197 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6150 (mt-10) REVERT: E 214 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5889 (pm20) REVERT: F 79 LEU cc_start: 0.1198 (OUTLIER) cc_final: 0.0939 (mt) REVERT: F 119 MET cc_start: 0.0352 (mmm) cc_final: -0.0018 (mmm) REVERT: G 119 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6429 (tp) REVERT: G 121 PHE cc_start: 0.7610 (m-10) cc_final: 0.7318 (m-10) REVERT: G 128 GLU cc_start: 0.6045 (pp20) cc_final: 0.5782 (pp20) REVERT: H 55 ARG cc_start: 0.7481 (mtt180) cc_final: 0.6833 (mtm-85) outliers start: 105 outliers final: 41 residues processed: 362 average time/residue: 1.4184 time to fit residues: 591.5350 Evaluate side-chains 308 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 372 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 56 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 202 optimal weight: 0.0870 chunk 212 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 203 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS D 352 GLN E 74 GLN F 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.180377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129677 restraints weight = 25047.659| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.06 r_work: 0.3236 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22742 Z= 0.184 Angle : 0.568 9.877 30984 Z= 0.300 Chirality : 0.043 0.154 3582 Planarity : 0.004 0.062 3707 Dihedral : 15.856 147.784 3547 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.10 % Allowed : 21.21 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2577 helix: 0.33 (0.15), residues: 1211 sheet: -0.35 (0.21), residues: 564 loop : -0.44 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 69 HIS 0.008 0.001 HIS E 93 PHE 0.021 0.002 PHE F 37 TYR 0.018 0.002 TYR H 166 ARG 0.005 0.000 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 1107) hydrogen bonds : angle 4.75853 ( 3197) covalent geometry : bond 0.00441 (22742) covalent geometry : angle 0.56797 (30984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 276 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8465 (tt) REVERT: A 187 GLU cc_start: 0.8403 (tt0) cc_final: 0.7972 (tp30) REVERT: A 189 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8933 (mt) REVERT: A 245 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.7978 (t) REVERT: A 351 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7347 (m170) REVERT: A 372 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.7818 (p) REVERT: C 332 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6809 (mt-10) REVERT: D 38 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8198 (mt-10) REVERT: E 74 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7259 (mm-40) REVERT: E 112 LEU cc_start: 0.7509 (mt) cc_final: 0.7202 (mt) REVERT: E 119 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.5964 (mpp) REVERT: E 134 ARG cc_start: 0.4309 (OUTLIER) cc_final: 0.2806 (mmt90) REVERT: E 197 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6409 (mt-10) REVERT: E 204 ASP cc_start: 0.6835 (m-30) cc_final: 0.6543 (t0) REVERT: E 268 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7389 (tpp80) REVERT: F 100 LEU cc_start: 0.1861 (OUTLIER) cc_final: 0.1453 (tt) REVERT: G 128 GLU cc_start: 0.6130 (pp20) cc_final: 0.5910 (pp20) REVERT: H 55 ARG cc_start: 0.7576 (mtt180) cc_final: 0.6961 (mtm-85) REVERT: H 63 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: H 139 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6999 (mm-30) REVERT: H 227 ILE cc_start: 0.5552 (OUTLIER) cc_final: 0.4751 (pp) REVERT: H 277 LEU cc_start: 0.6959 (tp) cc_final: 0.6585 (tp) outliers start: 121 outliers final: 51 residues processed: 366 average time/residue: 1.3284 time to fit residues: 557.8235 Evaluate side-chains 318 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 254 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 268 ARG Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 372 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 50 optimal weight: 4.9990 chunk 125 optimal weight: 0.0010 chunk 66 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 252 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 239 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 228 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS C 140 ASN C 184 HIS E 224 GLN ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.182826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132022 restraints weight = 25246.891| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.97 r_work: 0.3269 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22742 Z= 0.112 Angle : 0.502 9.658 30984 Z= 0.265 Chirality : 0.041 0.197 3582 Planarity : 0.004 0.056 3707 Dihedral : 15.673 139.842 3535 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.30 % Allowed : 22.09 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2577 helix: 0.63 (0.15), residues: 1207 sheet: -0.34 (0.21), residues: 565 loop : -0.35 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 42 HIS 0.007 0.001 HIS E 93 PHE 0.015 0.001 PHE G 40 TYR 0.016 0.001 TYR B 15 ARG 0.004 0.000 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 1107) hydrogen bonds : angle 4.52024 ( 3197) covalent geometry : bond 0.00248 (22742) covalent geometry : angle 0.50231 (30984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 271 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 187 GLU cc_start: 0.8383 (tt0) cc_final: 0.7973 (tp30) REVERT: A 245 SER cc_start: 0.8320 (p) cc_final: 0.7957 (t) REVERT: A 351 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7286 (m170) REVERT: A 372 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.7840 (p) REVERT: B 100 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7978 (ttmm) REVERT: C 73 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8198 (mmpt) REVERT: C 172 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6650 (pp20) REVERT: C 332 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6778 (mt-10) REVERT: D 38 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8208 (mt-10) REVERT: D 88 MET cc_start: 0.7977 (mtp) cc_final: 0.7773 (mtm) REVERT: E 74 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7300 (mm110) REVERT: E 204 ASP cc_start: 0.6974 (m-30) cc_final: 0.6548 (t0) REVERT: E 214 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6050 (pm20) REVERT: F 100 LEU cc_start: 0.1701 (OUTLIER) cc_final: 0.1324 (tt) REVERT: F 119 MET cc_start: 0.3077 (tpp) cc_final: 0.1783 (mmm) REVERT: G 202 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.5624 (t80) REVERT: H 55 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7085 (mtm-85) REVERT: H 63 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: H 227 ILE cc_start: 0.5725 (OUTLIER) cc_final: 0.4927 (pp) REVERT: H 277 LEU cc_start: 0.6942 (tp) cc_final: 0.6553 (tp) REVERT: H 284 MET cc_start: 0.6139 (tpt) cc_final: 0.5871 (tpt) REVERT: H 358 ASP cc_start: 0.7543 (m-30) cc_final: 0.6294 (p0) outliers start: 102 outliers final: 43 residues processed: 353 average time/residue: 1.3114 time to fit residues: 529.2120 Evaluate side-chains 307 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 372 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 107 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 156 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS E 103 ASN G 17 HIS ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.179460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125670 restraints weight = 25194.478| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.90 r_work: 0.3237 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22742 Z= 0.188 Angle : 0.557 10.214 30984 Z= 0.292 Chirality : 0.043 0.147 3582 Planarity : 0.004 0.059 3707 Dihedral : 15.793 148.999 3532 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.19 % Allowed : 21.67 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2577 helix: 0.49 (0.15), residues: 1213 sheet: -0.24 (0.21), residues: 561 loop : -0.44 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 296 HIS 0.008 0.001 HIS E 18 PHE 0.016 0.002 PHE A 279 TYR 0.022 0.001 TYR B 186 ARG 0.004 0.001 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 1107) hydrogen bonds : angle 4.55395 ( 3197) covalent geometry : bond 0.00454 (22742) covalent geometry : angle 0.55727 (30984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 255 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8457 (tt) REVERT: A 187 GLU cc_start: 0.8374 (tt0) cc_final: 0.7952 (tp30) REVERT: A 189 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8951 (mt) REVERT: A 245 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.7942 (t) REVERT: A 351 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7392 (m170) REVERT: A 372 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.7782 (p) REVERT: B 100 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8058 (ttmm) REVERT: B 180 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.8015 (tppt) REVERT: C 172 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6766 (pp20) REVERT: C 332 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6782 (mt-10) REVERT: D 38 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8197 (mt-10) REVERT: D 53 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8011 (mp) REVERT: E 74 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7357 (mm-40) REVERT: E 119 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6097 (mpp) REVERT: E 134 ARG cc_start: 0.4434 (OUTLIER) cc_final: 0.2918 (mmt90) REVERT: E 197 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6552 (mt-10) REVERT: E 204 ASP cc_start: 0.6969 (m-30) cc_final: 0.6618 (t0) REVERT: F 100 LEU cc_start: 0.1428 (OUTLIER) cc_final: 0.1127 (tt) REVERT: F 119 MET cc_start: 0.3037 (tpp) cc_final: 0.1939 (mmm) REVERT: G 155 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7781 (pp20) REVERT: H 55 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7128 (mtm-85) REVERT: H 63 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: H 139 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: H 227 ILE cc_start: 0.5684 (OUTLIER) cc_final: 0.4957 (pp) REVERT: H 277 LEU cc_start: 0.6960 (tp) cc_final: 0.6601 (tp) REVERT: H 358 ASP cc_start: 0.7590 (m-30) cc_final: 0.6254 (p0) outliers start: 123 outliers final: 63 residues processed: 348 average time/residue: 1.3071 time to fit residues: 520.9110 Evaluate side-chains 328 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 248 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 372 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS G 17 HIS ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.179457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127845 restraints weight = 25115.262| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.02 r_work: 0.3218 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22742 Z= 0.168 Angle : 0.544 10.288 30984 Z= 0.284 Chirality : 0.043 0.159 3582 Planarity : 0.004 0.070 3707 Dihedral : 15.824 149.218 3532 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.93 % Allowed : 22.01 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2577 helix: 0.54 (0.15), residues: 1212 sheet: -0.18 (0.21), residues: 562 loop : -0.43 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 296 HIS 0.007 0.001 HIS E 93 PHE 0.013 0.001 PHE F 37 TYR 0.023 0.001 TYR B 186 ARG 0.006 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 1107) hydrogen bonds : angle 4.48781 ( 3197) covalent geometry : bond 0.00404 (22742) covalent geometry : angle 0.54365 (30984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 254 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8475 (tt) REVERT: A 187 GLU cc_start: 0.8445 (tt0) cc_final: 0.8023 (tp30) REVERT: A 189 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8955 (mt) REVERT: A 245 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.8032 (t) REVERT: A 351 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7410 (m170) REVERT: A 372 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.7807 (p) REVERT: B 100 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8044 (ttmm) REVERT: B 272 ARG cc_start: 0.7700 (mtm110) cc_final: 0.7200 (mmm160) REVERT: C 172 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6824 (pp20) REVERT: C 332 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6722 (mt-10) REVERT: D 38 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8267 (mt-10) REVERT: D 273 GLU cc_start: 0.8260 (mp0) cc_final: 0.8046 (mp0) REVERT: E 74 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7376 (mm-40) REVERT: E 119 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.5954 (mpp) REVERT: E 204 ASP cc_start: 0.7008 (m-30) cc_final: 0.6630 (t0) REVERT: E 214 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6068 (pm20) REVERT: F 100 LEU cc_start: 0.1186 (OUTLIER) cc_final: 0.0928 (tt) REVERT: F 119 MET cc_start: 0.3148 (tpp) cc_final: 0.1988 (mmm) REVERT: G 202 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.5529 (t80) REVERT: H 55 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7143 (mtm-85) REVERT: H 63 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: H 139 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: H 227 ILE cc_start: 0.5831 (OUTLIER) cc_final: 0.5130 (pp) REVERT: H 251 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: H 277 LEU cc_start: 0.6889 (tp) cc_final: 0.6536 (tp) REVERT: H 358 ASP cc_start: 0.7525 (m-30) cc_final: 0.6308 (p0) outliers start: 117 outliers final: 63 residues processed: 340 average time/residue: 1.2992 time to fit residues: 505.2769 Evaluate side-chains 325 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 247 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 63 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 160 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 241 optimal weight: 0.0980 chunk 171 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 436 HIS B 8 GLN B 102 HIS E 103 ASN E 292 HIS G 17 HIS G 218 GLN H 53 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.182702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131116 restraints weight = 25043.198| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.04 r_work: 0.3266 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 22742 Z= 0.104 Angle : 0.506 9.625 30984 Z= 0.265 Chirality : 0.041 0.177 3582 Planarity : 0.004 0.057 3707 Dihedral : 15.695 139.232 3532 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.33 % Allowed : 23.95 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2577 helix: 0.76 (0.15), residues: 1216 sheet: -0.12 (0.21), residues: 564 loop : -0.26 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 259 HIS 0.007 0.001 HIS E 93 PHE 0.030 0.001 PHE A 279 TYR 0.021 0.001 TYR B 186 ARG 0.004 0.000 ARG D 175 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 1107) hydrogen bonds : angle 4.31625 ( 3197) covalent geometry : bond 0.00233 (22742) covalent geometry : angle 0.50556 (30984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 270 time to evaluate : 2.257 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8404 (tt) REVERT: A 187 GLU cc_start: 0.8453 (tt0) cc_final: 0.8022 (tp30) REVERT: A 241 ASP cc_start: 0.7235 (m-30) cc_final: 0.6944 (m-30) REVERT: A 245 SER cc_start: 0.8302 (p) cc_final: 0.8036 (t) REVERT: A 351 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7368 (m170) REVERT: B 100 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7767 (tptm) REVERT: B 272 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7133 (mmm160) REVERT: C 91 ASP cc_start: 0.8040 (m-30) cc_final: 0.7502 (p0) REVERT: C 172 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6690 (pp20) REVERT: C 245 LYS cc_start: 0.8009 (mtpt) cc_final: 0.7776 (mppt) REVERT: C 332 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6676 (mt-10) REVERT: D 38 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8203 (mt-10) REVERT: E 74 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7366 (mm-40) REVERT: E 119 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6774 (mmt) REVERT: E 204 ASP cc_start: 0.7005 (m-30) cc_final: 0.6600 (t0) REVERT: F 18 LEU cc_start: 0.2205 (OUTLIER) cc_final: 0.1932 (mm) REVERT: F 19 LEU cc_start: 0.3622 (OUTLIER) cc_final: 0.3408 (mm) REVERT: F 100 LEU cc_start: 0.1210 (OUTLIER) cc_final: 0.0996 (tt) REVERT: F 119 MET cc_start: 0.3262 (tpp) cc_final: 0.2139 (mmm) REVERT: F 413 LYS cc_start: 0.5542 (OUTLIER) cc_final: 0.5050 (ttpp) REVERT: G 202 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.5487 (t80) REVERT: H 55 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7143 (mtm-85) REVERT: H 63 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: H 139 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6952 (mm-30) REVERT: H 227 ILE cc_start: 0.5809 (OUTLIER) cc_final: 0.5126 (pp) REVERT: H 251 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7119 (mm-30) REVERT: H 277 LEU cc_start: 0.6792 (tp) cc_final: 0.6439 (tp) REVERT: H 358 ASP cc_start: 0.7559 (m-30) cc_final: 0.6309 (p0) outliers start: 79 outliers final: 40 residues processed: 327 average time/residue: 1.5031 time to fit residues: 559.1007 Evaluate side-chains 297 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 180 optimal weight: 0.0060 chunk 79 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 436 HIS B 102 HIS E 103 ASN G 17 HIS G 218 GLN H 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128934 restraints weight = 25170.555| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.91 r_work: 0.3272 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22742 Z= 0.138 Angle : 0.527 10.198 30984 Z= 0.275 Chirality : 0.042 0.172 3582 Planarity : 0.004 0.058 3707 Dihedral : 15.674 140.044 3530 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.22 % Allowed : 23.27 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2577 helix: 0.75 (0.15), residues: 1226 sheet: -0.08 (0.22), residues: 557 loop : -0.31 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 296 HIS 0.007 0.001 HIS E 93 PHE 0.012 0.001 PHE A 376 TYR 0.024 0.001 TYR B 186 ARG 0.005 0.000 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 1107) hydrogen bonds : angle 4.32340 ( 3197) covalent geometry : bond 0.00325 (22742) covalent geometry : angle 0.52705 (30984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 254 time to evaluate : 7.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8380 (tt) REVERT: A 187 GLU cc_start: 0.8387 (tt0) cc_final: 0.7968 (tp30) REVERT: A 241 ASP cc_start: 0.7270 (m-30) cc_final: 0.6985 (m-30) REVERT: A 245 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7962 (t) REVERT: A 351 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7378 (m170) REVERT: A 372 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.7879 (p) REVERT: B 100 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7761 (tptm) REVERT: B 272 ARG cc_start: 0.7548 (mtm110) cc_final: 0.7102 (mmm160) REVERT: C 172 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6705 (pp20) REVERT: C 332 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6703 (mt-10) REVERT: D 38 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8216 (mt-10) REVERT: E 74 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7344 (mm110) REVERT: E 204 ASP cc_start: 0.6996 (m-30) cc_final: 0.6618 (t0) REVERT: F 100 LEU cc_start: 0.1265 (OUTLIER) cc_final: 0.1058 (tt) REVERT: F 119 MET cc_start: 0.3271 (tpp) cc_final: 0.2119 (mmm) REVERT: F 413 LYS cc_start: 0.5461 (OUTLIER) cc_final: 0.5009 (ttpp) REVERT: G 202 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.5500 (t80) REVERT: H 55 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7117 (mtm-85) REVERT: H 63 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: H 139 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: H 227 ILE cc_start: 0.5770 (OUTLIER) cc_final: 0.5139 (pp) REVERT: H 251 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: H 277 LEU cc_start: 0.6800 (tp) cc_final: 0.6422 (tp) REVERT: H 358 ASP cc_start: 0.7484 (m-30) cc_final: 0.6258 (p0) outliers start: 100 outliers final: 60 residues processed: 327 average time/residue: 1.9420 time to fit residues: 729.4965 Evaluate side-chains 315 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 242 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 237 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS G 17 HIS G 218 GLN H 53 GLN H 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.180071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126726 restraints weight = 25053.610| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.89 r_work: 0.3245 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22742 Z= 0.151 Angle : 0.533 10.496 30984 Z= 0.279 Chirality : 0.042 0.168 3582 Planarity : 0.004 0.059 3707 Dihedral : 15.697 142.541 3528 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.79 % Allowed : 23.86 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2577 helix: 0.79 (0.15), residues: 1217 sheet: -0.05 (0.22), residues: 558 loop : -0.38 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 296 HIS 0.007 0.001 HIS E 93 PHE 0.025 0.001 PHE A 279 TYR 0.024 0.001 TYR B 186 ARG 0.008 0.000 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 1107) hydrogen bonds : angle 4.33637 ( 3197) covalent geometry : bond 0.00361 (22742) covalent geometry : angle 0.53310 (30984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 247 time to evaluate : 2.617 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8414 (tt) REVERT: A 187 GLU cc_start: 0.8405 (tt0) cc_final: 0.8018 (tp30) REVERT: A 241 ASP cc_start: 0.7322 (m-30) cc_final: 0.7011 (m-30) REVERT: A 245 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8096 (t) REVERT: A 307 GLU cc_start: 0.8155 (tp30) cc_final: 0.7822 (tp30) REVERT: A 351 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7455 (m170) REVERT: A 372 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.7927 (p) REVERT: B 87 ASP cc_start: 0.7951 (t70) cc_final: 0.7191 (p0) REVERT: B 100 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7923 (tptm) REVERT: B 272 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7208 (mmm160) REVERT: B 301 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: C 172 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6799 (pp20) REVERT: C 245 LYS cc_start: 0.7952 (mppt) cc_final: 0.7325 (mttt) REVERT: C 256 TRP cc_start: 0.9382 (OUTLIER) cc_final: 0.9086 (m100) REVERT: C 332 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6758 (mt-10) REVERT: D 38 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8252 (mt-10) REVERT: E 74 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7380 (mm110) REVERT: E 204 ASP cc_start: 0.7032 (m-30) cc_final: 0.6669 (t0) REVERT: E 214 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.6186 (pm20) REVERT: F 100 LEU cc_start: 0.1165 (OUTLIER) cc_final: 0.0959 (tt) REVERT: F 119 MET cc_start: 0.3295 (tpp) cc_final: 0.2130 (mmm) REVERT: G 176 LYS cc_start: 0.8119 (tptm) cc_final: 0.7009 (pttm) REVERT: G 202 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.5467 (t80) REVERT: H 55 ARG cc_start: 0.7651 (mtt180) cc_final: 0.7205 (mtm-85) REVERT: H 63 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: H 139 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: H 227 ILE cc_start: 0.5883 (OUTLIER) cc_final: 0.5251 (pp) REVERT: H 251 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: H 277 LEU cc_start: 0.6841 (tp) cc_final: 0.6505 (tp) REVERT: H 358 ASP cc_start: 0.7532 (m-30) cc_final: 0.6335 (p0) outliers start: 90 outliers final: 60 residues processed: 315 average time/residue: 1.3624 time to fit residues: 489.3073 Evaluate side-chains 312 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 237 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 82 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 6 optimal weight: 0.3980 chunk 186 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS D 338 ASN E 103 ASN G 17 HIS G 218 GLN H 53 GLN H 365 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.182460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129516 restraints weight = 25081.824| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.90 r_work: 0.3292 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22742 Z= 0.107 Angle : 0.506 9.979 30984 Z= 0.265 Chirality : 0.041 0.154 3582 Planarity : 0.004 0.059 3707 Dihedral : 15.610 136.478 3528 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.41 % Allowed : 24.33 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2577 helix: 0.97 (0.15), residues: 1212 sheet: 0.02 (0.22), residues: 563 loop : -0.23 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 259 HIS 0.006 0.001 HIS E 93 PHE 0.018 0.001 PHE G 154 TYR 0.022 0.001 TYR B 186 ARG 0.007 0.000 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 1107) hydrogen bonds : angle 4.22489 ( 3197) covalent geometry : bond 0.00240 (22742) covalent geometry : angle 0.50622 (30984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 254 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8348 (tt) REVERT: A 187 GLU cc_start: 0.8409 (tt0) cc_final: 0.7992 (tp30) REVERT: A 241 ASP cc_start: 0.7233 (m-30) cc_final: 0.6945 (m-30) REVERT: A 245 SER cc_start: 0.8213 (p) cc_final: 0.7998 (t) REVERT: A 307 GLU cc_start: 0.8158 (tp30) cc_final: 0.7858 (tp30) REVERT: B 87 ASP cc_start: 0.7901 (t70) cc_final: 0.7155 (p0) REVERT: B 100 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7763 (tptm) REVERT: B 272 ARG cc_start: 0.7504 (mtm110) cc_final: 0.7065 (mmm160) REVERT: B 301 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: C 73 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8130 (mmpt) REVERT: C 91 ASP cc_start: 0.7997 (m-30) cc_final: 0.7512 (p0) REVERT: C 172 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6616 (pp20) REVERT: C 332 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6574 (mt-10) REVERT: D 38 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8229 (mt-10) REVERT: E 74 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7296 (mm110) REVERT: E 204 ASP cc_start: 0.6954 (m-30) cc_final: 0.6569 (t0) REVERT: E 214 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.6176 (pm20) REVERT: F 19 LEU cc_start: 0.3453 (mm) cc_final: 0.2982 (pt) REVERT: F 43 THR cc_start: 0.1742 (OUTLIER) cc_final: 0.1453 (m) REVERT: F 119 MET cc_start: 0.3265 (tpp) cc_final: 0.2134 (mmm) REVERT: F 413 LYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5107 (ttpp) REVERT: G 202 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.5360 (t80) REVERT: H 55 ARG cc_start: 0.7569 (mtt180) cc_final: 0.7113 (mtm-85) REVERT: H 63 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: H 139 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6880 (mm-30) REVERT: H 227 ILE cc_start: 0.5869 (OUTLIER) cc_final: 0.5241 (pp) REVERT: H 242 ASP cc_start: 0.7331 (m-30) cc_final: 0.7102 (t0) REVERT: H 251 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: H 277 LEU cc_start: 0.6777 (tp) cc_final: 0.6431 (tp) REVERT: H 358 ASP cc_start: 0.7545 (m-30) cc_final: 0.6296 (p0) outliers start: 81 outliers final: 49 residues processed: 316 average time/residue: 1.4136 time to fit residues: 515.6627 Evaluate side-chains 315 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 253 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 218 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 49 optimal weight: 0.0570 chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS G 17 HIS G 218 GLN H 53 GLN H 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.182264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129737 restraints weight = 24999.605| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.86 r_work: 0.3294 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22742 Z= 0.114 Angle : 0.511 10.169 30984 Z= 0.267 Chirality : 0.041 0.150 3582 Planarity : 0.004 0.059 3707 Dihedral : 15.542 134.407 3526 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.12 % Allowed : 24.66 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2577 helix: 0.99 (0.15), residues: 1219 sheet: 0.04 (0.22), residues: 563 loop : -0.23 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 259 HIS 0.006 0.001 HIS E 93 PHE 0.027 0.001 PHE A 279 TYR 0.022 0.001 TYR B 186 ARG 0.007 0.000 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 1107) hydrogen bonds : angle 4.20791 ( 3197) covalent geometry : bond 0.00261 (22742) covalent geometry : angle 0.51143 (30984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19321.80 seconds wall clock time: 335 minutes 29.11 seconds (20129.11 seconds total)