Starting phenix.real_space_refine on Wed Jun 18 19:49:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v2w_31669/06_2025/7v2w_31669.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v2w_31669/06_2025/7v2w_31669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v2w_31669/06_2025/7v2w_31669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v2w_31669/06_2025/7v2w_31669.map" model { file = "/net/cci-nas-00/data/ceres_data/7v2w_31669/06_2025/7v2w_31669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v2w_31669/06_2025/7v2w_31669.cif" } resolution = 3.2 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= 0.002 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 13799 2.51 5 N 3598 2.21 5 O 4134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 187 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21619 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4942 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 22, 'TRANS': 570} Chain breaks: 1 Chain: "G" Number of atoms: 9824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1207, 9824 Classifications: {'peptide': 1207} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1173} Chain breaks: 1 Chain: "H" Number of atoms: 2979 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 379, 2979 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 8, 'TRANS': 370} Chain breaks: 1 Chain: "I" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1941 Classifications: {'peptide': 240} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1933 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Time building chain proxies: 14.54, per 1000 atoms: 0.67 Number of scatterers: 21619 At special positions: 0 Unit cell: (179.3, 117.7, 212.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 4134 8.00 N 3598 7.00 C 13799 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: 7.73 Conformation dependent library (CDL) restraints added in 3.9 seconds 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 10 sheets defined 57.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'F' and resid 3 through 21 removed outlier: 3.506A pdb=" N SER F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY F 13 " --> pdb=" O GLN F 9 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS F 17 " --> pdb=" O GLY F 13 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.586A pdb=" N PHE F 46 " --> pdb=" O VAL F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 78 removed outlier: 4.006A pdb=" N ASP F 66 " --> pdb=" O ASP F 62 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 106 removed outlier: 3.751A pdb=" N GLU F 90 " --> pdb=" O GLU F 86 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY F 92 " --> pdb=" O ASN F 88 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN F 95 " --> pdb=" O LYS F 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 131 removed outlier: 3.785A pdb=" N PHE F 121 " --> pdb=" O GLY F 117 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU F 122 " --> pdb=" O ASN F 118 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 128 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP F 129 " --> pdb=" O SER F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 141 removed outlier: 3.602A pdb=" N LEU F 138 " --> pdb=" O PRO F 134 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 removed outlier: 3.733A pdb=" N SER F 146 " --> pdb=" O PRO F 142 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 180 through 191 removed outlier: 3.796A pdb=" N ILE F 184 " --> pdb=" O HIS F 180 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 185 " --> pdb=" O TRP F 181 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 186 " --> pdb=" O ASN F 182 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 214 removed outlier: 3.540A pdb=" N GLU F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.562A pdb=" N ASN F 260 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 262 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR F 264 " --> pdb=" O ASN F 260 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS F 265 " --> pdb=" O PHE F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 removed outlier: 3.607A pdb=" N PHE F 275 " --> pdb=" O ILE F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 Proline residue: F 290 - end of helix removed outlier: 3.562A pdb=" N ASP F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU F 297 " --> pdb=" O ASP F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 313 removed outlier: 3.825A pdb=" N ILE F 306 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS F 307 " --> pdb=" O TYR F 303 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR F 312 " --> pdb=" O MET F 308 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG F 313 " --> pdb=" O ASN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 removed outlier: 3.857A pdb=" N GLU F 318 " --> pdb=" O TYR F 314 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA F 319 " --> pdb=" O SER F 315 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN F 321 " --> pdb=" O GLU F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 348 removed outlier: 3.534A pdb=" N MET F 347 " --> pdb=" O ASN F 343 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP F 348 " --> pdb=" O ALA F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 354 Processing helix chain 'F' and resid 356 through 361 removed outlier: 3.570A pdb=" N LYS F 360 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 386 removed outlier: 3.915A pdb=" N TYR F 383 " --> pdb=" O THR F 379 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 386 " --> pdb=" O LEU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 405 removed outlier: 3.854A pdb=" N THR F 405 " --> pdb=" O GLN F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 414 Processing helix chain 'F' and resid 417 through 428 removed outlier: 3.637A pdb=" N LYS F 423 " --> pdb=" O ARG F 419 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER F 424 " --> pdb=" O ASN F 420 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS F 425 " --> pdb=" O PHE F 421 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR F 426 " --> pdb=" O TYR F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 449 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.661A pdb=" N SER F 453 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR F 454 " --> pdb=" O ASN F 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 449 through 454' Processing helix chain 'F' and resid 459 through 467 removed outlier: 3.529A pdb=" N PHE F 463 " --> pdb=" O ARG F 459 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS F 467 " --> pdb=" O PHE F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 481 removed outlier: 3.651A pdb=" N ARG F 473 " --> pdb=" O PRO F 469 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 474 " --> pdb=" O ASP F 470 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER F 480 " --> pdb=" O ARG F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 492 removed outlier: 3.518A pdb=" N ALA F 488 " --> pdb=" O LYS F 484 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE F 490 " --> pdb=" O THR F 486 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP F 491 " --> pdb=" O THR F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 532 removed outlier: 3.664A pdb=" N ASN F 529 " --> pdb=" O ASN F 525 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP F 532 " --> pdb=" O ILE F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 3.751A pdb=" N GLU F 542 " --> pdb=" O LEU F 538 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN F 543 " --> pdb=" O ASP F 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 538 through 543' Processing helix chain 'F' and resid 547 through 563 removed outlier: 3.571A pdb=" N ALA F 554 " --> pdb=" O GLY F 550 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN F 556 " --> pdb=" O TYR F 552 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP F 559 " --> pdb=" O ALA F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 584 removed outlier: 3.700A pdb=" N ARG F 584 " --> pdb=" O TRP F 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 15 removed outlier: 3.824A pdb=" N SER G 8 " --> pdb=" O GLN G 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU G 13 " --> pdb=" O LYS G 9 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN G 15 " --> pdb=" O ASN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 48 removed outlier: 4.090A pdb=" N LYS G 42 " --> pdb=" O PRO G 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 44 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP G 47 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE G 48 " --> pdb=" O LEU G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 74 removed outlier: 3.634A pdb=" N PHE G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE G 69 " --> pdb=" O PHE G 65 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN G 73 " --> pdb=" O PHE G 69 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 97 removed outlier: 3.571A pdb=" N PHE G 89 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU G 92 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN G 95 " --> pdb=" O ASN G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 117 removed outlier: 3.525A pdb=" N VAL G 113 " --> pdb=" O MET G 109 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 130 removed outlier: 3.580A pdb=" N THR G 125 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 142 Processing helix chain 'G' and resid 143 through 147 removed outlier: 4.046A pdb=" N SER G 146 " --> pdb=" O SER G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 166 removed outlier: 3.657A pdb=" N LEU G 158 " --> pdb=" O GLN G 154 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS G 163 " --> pdb=" O ARG G 159 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS G 164 " --> pdb=" O HIS G 160 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 193 removed outlier: 3.586A pdb=" N ALA G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 216 removed outlier: 3.836A pdb=" N LYS G 207 " --> pdb=" O SER G 203 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 231 removed outlier: 3.938A pdb=" N LEU G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 247 removed outlier: 3.629A pdb=" N ILE G 243 " --> pdb=" O TYR G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 282 removed outlier: 3.665A pdb=" N SER G 279 " --> pdb=" O ALA G 275 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE G 280 " --> pdb=" O ASN G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 301 Processing helix chain 'G' and resid 302 through 307 removed outlier: 3.597A pdb=" N LYS G 306 " --> pdb=" O CYS G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 317 Processing helix chain 'G' and resid 322 through 341 removed outlier: 3.515A pdb=" N GLN G 327 " --> pdb=" O MET G 323 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G 328 " --> pdb=" O GLU G 324 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR G 329 " --> pdb=" O PHE G 325 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN G 331 " --> pdb=" O GLN G 327 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU G 336 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU G 340 " --> pdb=" O GLU G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 396 Processing helix chain 'G' and resid 397 through 399 No H-bonds generated for 'chain 'G' and resid 397 through 399' Processing helix chain 'G' and resid 403 through 415 removed outlier: 3.616A pdb=" N GLU G 409 " --> pdb=" O ILE G 405 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU G 412 " --> pdb=" O LEU G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 425 removed outlier: 3.642A pdb=" N VAL G 423 " --> pdb=" O PRO G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 457 removed outlier: 3.559A pdb=" N LEU G 441 " --> pdb=" O LEU G 437 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY G 442 " --> pdb=" O SER G 438 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL G 444 " --> pdb=" O TYR G 440 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU G 446 " --> pdb=" O GLY G 442 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR G 447 " --> pdb=" O ARG G 443 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN G 450 " --> pdb=" O GLU G 446 " (cutoff:3.500A) Proline residue: G 451 - end of helix removed outlier: 3.534A pdb=" N SER G 455 " --> pdb=" O PRO G 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR G 457 " --> pdb=" O TYR G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 463 removed outlier: 3.602A pdb=" N LYS G 463 " --> pdb=" O SER G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 468 removed outlier: 3.881A pdb=" N ALA G 468 " --> pdb=" O ASP G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 Processing helix chain 'G' and resid 538 through 541 Processing helix chain 'G' and resid 542 through 560 removed outlier: 3.557A pdb=" N LYS G 548 " --> pdb=" O THR G 544 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER G 550 " --> pdb=" O LEU G 546 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG G 551 " --> pdb=" O SER G 547 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 559 " --> pdb=" O ALA G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 566 through 580 removed outlier: 3.753A pdb=" N ASP G 571 " --> pdb=" O HIS G 567 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP G 575 " --> pdb=" O ASP G 571 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR G 576 " --> pdb=" O LYS G 572 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE G 580 " --> pdb=" O TYR G 576 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 586 removed outlier: 3.906A pdb=" N SER G 586 " --> pdb=" O PHE G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 591 through 600 removed outlier: 3.539A pdb=" N THR G 595 " --> pdb=" O ASN G 591 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 596 " --> pdb=" O PRO G 592 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL G 598 " --> pdb=" O ALA G 594 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 605 removed outlier: 3.538A pdb=" N PHE G 604 " --> pdb=" O LEU G 601 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE G 605 " --> pdb=" O MET G 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 605' Processing helix chain 'G' and resid 606 through 617 removed outlier: 3.974A pdb=" N ILE G 613 " --> pdb=" O LYS G 609 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR G 614 " --> pdb=" O ARG G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 643 removed outlier: 3.697A pdb=" N LYS G 629 " --> pdb=" O ILE G 625 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER G 631 " --> pdb=" O PRO G 627 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG G 637 " --> pdb=" O ASN G 633 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER G 641 " --> pdb=" O ARG G 637 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 665 removed outlier: 3.547A pdb=" N ARG G 657 " --> pdb=" O LYS G 653 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS G 660 " --> pdb=" O ARG G 656 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU G 661 " --> pdb=" O ARG G 657 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN G 665 " --> pdb=" O LEU G 661 " (cutoff:3.500A) Processing helix chain 'G' and resid 665 through 670 removed outlier: 3.694A pdb=" N SER G 669 " --> pdb=" O ASN G 665 " (cutoff:3.500A) Processing helix chain 'G' and resid 670 through 675 Processing helix chain 'G' and resid 683 through 691 removed outlier: 3.877A pdb=" N TYR G 689 " --> pdb=" O GLU G 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 692 through 694 No H-bonds generated for 'chain 'G' and resid 692 through 694' Processing helix chain 'G' and resid 695 through 711 removed outlier: 3.636A pdb=" N ASP G 700 " --> pdb=" O ASP G 696 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 702 " --> pdb=" O ALA G 698 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN G 703 " --> pdb=" O TYR G 699 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE G 704 " --> pdb=" O ASP G 700 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR G 711 " --> pdb=" O LEU G 707 " (cutoff:3.500A) Processing helix chain 'G' and resid 726 through 742 removed outlier: 3.670A pdb=" N ARG G 730 " --> pdb=" O MET G 726 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER G 732 " --> pdb=" O VAL G 728 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE G 734 " --> pdb=" O ARG G 730 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 739 " --> pdb=" O ILE G 735 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS G 740 " --> pdb=" O ALA G 736 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN G 741 " --> pdb=" O GLY G 737 " (cutoff:3.500A) Processing helix chain 'G' and resid 750 through 761 removed outlier: 3.655A pdb=" N LYS G 756 " --> pdb=" O THR G 752 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS G 759 " --> pdb=" O LEU G 755 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN G 760 " --> pdb=" O LYS G 756 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 776 removed outlier: 3.747A pdb=" N SER G 767 " --> pdb=" O ILE G 763 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 769 " --> pdb=" O ALA G 765 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU G 771 " --> pdb=" O SER G 767 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE G 774 " --> pdb=" O LYS G 770 " (cutoff:3.500A) Processing helix chain 'G' and resid 786 through 791 removed outlier: 3.885A pdb=" N LEU G 791 " --> pdb=" O MET G 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 797 through 807 removed outlier: 3.928A pdb=" N GLN G 801 " --> pdb=" O SER G 797 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS G 805 " --> pdb=" O GLN G 801 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 806 " --> pdb=" O TYR G 802 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 828 removed outlier: 3.628A pdb=" N SER G 818 " --> pdb=" O ASN G 814 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG G 820 " --> pdb=" O VAL G 816 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER G 823 " --> pdb=" O SER G 819 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE G 824 " --> pdb=" O ARG G 820 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE G 825 " --> pdb=" O LEU G 821 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR G 826 " --> pdb=" O THR G 822 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN G 828 " --> pdb=" O PHE G 824 " (cutoff:3.500A) Processing helix chain 'G' and resid 833 through 845 removed outlier: 3.516A pdb=" N THR G 840 " --> pdb=" O LEU G 836 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN G 842 " --> pdb=" O LEU G 838 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA G 845 " --> pdb=" O LEU G 841 " (cutoff:3.500A) Processing helix chain 'G' and resid 853 through 877 removed outlier: 3.573A pdb=" N CYS G 859 " --> pdb=" O LEU G 855 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP G 860 " --> pdb=" O SER G 856 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN G 863 " --> pdb=" O CYS G 859 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU G 866 " --> pdb=" O MET G 862 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU G 872 " --> pdb=" O SER G 868 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS G 875 " --> pdb=" O GLU G 871 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS G 876 " --> pdb=" O LEU G 872 " (cutoff:3.500A) Processing helix chain 'G' and resid 879 through 886 removed outlier: 3.953A pdb=" N GLU G 883 " --> pdb=" O GLY G 879 " (cutoff:3.500A) Processing helix chain 'G' and resid 899 through 907 removed outlier: 3.546A pdb=" N PHE G 904 " --> pdb=" O THR G 900 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS G 905 " --> pdb=" O PRO G 901 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE G 906 " --> pdb=" O TRP G 902 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP G 907 " --> pdb=" O THR G 903 " (cutoff:3.500A) Processing helix chain 'G' and resid 909 through 914 Processing helix chain 'G' and resid 921 through 928 removed outlier: 3.626A pdb=" N GLU G 925 " --> pdb=" O PHE G 921 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU G 926 " --> pdb=" O SER G 922 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE G 927 " --> pdb=" O ILE G 923 " (cutoff:3.500A) Processing helix chain 'G' and resid 941 through 951 removed outlier: 4.286A pdb=" N THR G 947 " --> pdb=" O ASP G 943 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP G 949 " --> pdb=" O PHE G 945 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU G 951 " --> pdb=" O THR G 947 " (cutoff:3.500A) Processing helix chain 'G' and resid 960 through 965 removed outlier: 3.734A pdb=" N ASP G 964 " --> pdb=" O LYS G 960 " (cutoff:3.500A) Processing helix chain 'G' and resid 966 through 974 removed outlier: 3.509A pdb=" N SER G 971 " --> pdb=" O LYS G 967 " (cutoff:3.500A) Processing helix chain 'G' and resid 979 through 1013 removed outlier: 4.004A pdb=" N LYS G 983 " --> pdb=" O SER G 979 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP G 992 " --> pdb=" O ASN G 988 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE G 993 " --> pdb=" O GLN G 989 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU G 994 " --> pdb=" O ILE G 990 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR G1007 " --> pdb=" O ALA G1003 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G1010 " --> pdb=" O LYS G1006 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER G1012 " --> pdb=" O SER G1008 " (cutoff:3.500A) Processing helix chain 'G' and resid 1014 through 1019 removed outlier: 3.597A pdb=" N ASN G1019 " --> pdb=" O SER G1015 " (cutoff:3.500A) Processing helix chain 'G' and resid 1023 through 1034 removed outlier: 3.585A pdb=" N GLN G1032 " --> pdb=" O LYS G1028 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS G1034 " --> pdb=" O PHE G1030 " (cutoff:3.500A) Processing helix chain 'G' and resid 1034 through 1042 removed outlier: 3.506A pdb=" N ARG G1038 " --> pdb=" O CYS G1034 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE G1041 " --> pdb=" O PRO G1037 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER G1042 " --> pdb=" O ARG G1038 " (cutoff:3.500A) Processing helix chain 'G' and resid 1042 through 1057 removed outlier: 3.675A pdb=" N LEU G1047 " --> pdb=" O PRO G1043 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE G1048 " --> pdb=" O SER G1044 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER G1049 " --> pdb=" O ASP G1045 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER G1050 " --> pdb=" O ALA G1046 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE G1053 " --> pdb=" O SER G1049 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE G1054 " --> pdb=" O SER G1050 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE G1057 " --> pdb=" O ILE G1053 " (cutoff:3.500A) Processing helix chain 'G' and resid 1058 through 1072 removed outlier: 3.565A pdb=" N MET G1063 " --> pdb=" O THR G1059 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER G1064 " --> pdb=" O GLU G1060 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN G1067 " --> pdb=" O MET G1063 " (cutoff:3.500A) Processing helix chain 'G' and resid 1074 through 1079 Processing helix chain 'G' and resid 1083 through 1095 removed outlier: 3.708A pdb=" N GLY G1088 " --> pdb=" O SER G1084 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU G1090 " --> pdb=" O GLU G1086 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE G1094 " --> pdb=" O LEU G1090 " (cutoff:3.500A) Processing helix chain 'G' and resid 1097 through 1106 removed outlier: 3.556A pdb=" N LYS G1103 " --> pdb=" O LYS G1099 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET G1104 " --> pdb=" O LYS G1100 " (cutoff:3.500A) Processing helix chain 'G' and resid 1111 through 1134 removed outlier: 3.767A pdb=" N THR G1126 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU G1127 " --> pdb=" O SER G1123 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP G1131 " --> pdb=" O GLU G1127 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU G1132 " --> pdb=" O GLN G1128 " (cutoff:3.500A) Processing helix chain 'G' and resid 1138 through 1152 removed outlier: 4.141A pdb=" N GLY G1144 " --> pdb=" O SER G1140 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N HIS G1150 " --> pdb=" O GLU G1146 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL G1151 " --> pdb=" O PHE G1147 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR G1152 " --> pdb=" O MET G1148 " (cutoff:3.500A) Processing helix chain 'G' and resid 1153 through 1155 No H-bonds generated for 'chain 'G' and resid 1153 through 1155' Processing helix chain 'G' and resid 1158 through 1168 removed outlier: 3.973A pdb=" N ILE G1162 " --> pdb=" O VAL G1158 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN G1163 " --> pdb=" O LYS G1159 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G1164 " --> pdb=" O ALA G1160 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR G1167 " --> pdb=" O GLN G1163 " (cutoff:3.500A) Processing helix chain 'G' and resid 1171 through 1176 removed outlier: 3.773A pdb=" N GLU G1176 " --> pdb=" O ASN G1172 " (cutoff:3.500A) Processing helix chain 'G' and resid 1181 through 1194 removed outlier: 3.818A pdb=" N SER G1185 " --> pdb=" O ILE G1181 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA G1187 " --> pdb=" O LEU G1183 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY G1190 " --> pdb=" O SER G1186 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS G1191 " --> pdb=" O ALA G1187 " (cutoff:3.500A) Processing helix chain 'G' and resid 1211 through 1231 removed outlier: 3.733A pdb=" N ILE G1218 " --> pdb=" O GLU G1214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET G1221 " --> pdb=" O ARG G1217 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU G1223 " --> pdb=" O ARG G1219 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS G1227 " --> pdb=" O LEU G1223 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN G1228 " --> pdb=" O GLU G1224 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR G1231 " --> pdb=" O LYS G1227 " (cutoff:3.500A) Processing helix chain 'G' and resid 1241 through 1255 removed outlier: 3.649A pdb=" N GLN G1245 " --> pdb=" O ALA G1241 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU G1247 " --> pdb=" O ARG G1243 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN G1252 " --> pdb=" O LEU G1248 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN G1255 " --> pdb=" O SER G1251 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 removed outlier: 4.519A pdb=" N GLN H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 8 through 12' Processing helix chain 'H' and resid 16 through 28 removed outlier: 3.883A pdb=" N ALA H 21 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS H 26 " --> pdb=" O SER H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 54 removed outlier: 3.525A pdb=" N ARG H 51 " --> pdb=" O HIS H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 373 through 389 removed outlier: 3.808A pdb=" N ASP H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP H 382 " --> pdb=" O LYS H 378 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE H 386 " --> pdb=" O ASP H 382 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU H 387 " --> pdb=" O ASN H 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 17 removed outlier: 4.088A pdb=" N VAL I 11 " --> pdb=" O GLN I 7 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS I 14 " --> pdb=" O GLN I 10 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR I 17 " --> pdb=" O THR I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 42 removed outlier: 3.889A pdb=" N ILE I 30 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 36 " --> pdb=" O GLY I 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE I 42 " --> pdb=" O THR I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 78 removed outlier: 3.597A pdb=" N GLU I 66 " --> pdb=" O SER I 62 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG I 71 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE I 72 " --> pdb=" O ALA I 68 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 73 " --> pdb=" O HIS I 69 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 98 removed outlier: 3.503A pdb=" N LYS I 83 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP I 86 " --> pdb=" O LYS I 82 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP I 89 " --> pdb=" O ALA I 85 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU I 90 " --> pdb=" O ASP I 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR I 91 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR I 96 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 97 " --> pdb=" O GLN I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 142 removed outlier: 4.024A pdb=" N ILE I 113 " --> pdb=" O ASP I 109 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU I 117 " --> pdb=" O ILE I 113 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 124 " --> pdb=" O ARG I 120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR I 128 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP I 129 " --> pdb=" O GLN I 125 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN I 132 " --> pdb=" O TYR I 128 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL I 133 " --> pdb=" O ASP I 129 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU I 139 " --> pdb=" O ASN I 135 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY I 140 " --> pdb=" O ARG I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 156 removed outlier: 3.648A pdb=" N GLU I 156 " --> pdb=" O ARG I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 168 removed outlier: 3.541A pdb=" N LYS I 165 " --> pdb=" O THR I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 235 removed outlier: 3.740A pdb=" N SER I 204 " --> pdb=" O LYS I 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER I 208 " --> pdb=" O SER I 204 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN I 218 " --> pdb=" O GLU I 214 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER I 221 " --> pdb=" O ARG I 217 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR I 223 " --> pdb=" O GLU I 219 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU I 228 " --> pdb=" O LYS I 224 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE I 233 " --> pdb=" O ARG I 229 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY I 235 " --> pdb=" O ALA I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 250 removed outlier: 3.924A pdb=" N LYS I 247 " --> pdb=" O GLU I 243 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG I 248 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 13 Processing helix chain 'J' and resid 14 through 37 removed outlier: 3.794A pdb=" N GLN J 18 " --> pdb=" O CYS J 14 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU J 20 " --> pdb=" O GLU J 16 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN J 29 " --> pdb=" O THR J 25 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE J 30 " --> pdb=" O HIS J 26 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 52 removed outlier: 3.530A pdb=" N SER J 50 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 79 removed outlier: 3.664A pdb=" N LEU J 57 " --> pdb=" O LYS J 53 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG J 59 " --> pdb=" O PRO J 55 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU J 60 " --> pdb=" O ASP J 56 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE J 66 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG J 67 " --> pdb=" O ASN J 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR J 75 " --> pdb=" O ASP J 71 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG J 76 " --> pdb=" O LYS J 72 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU J 77 " --> pdb=" O TYR J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 86 Processing helix chain 'J' and resid 90 through 94 removed outlier: 3.739A pdb=" N GLY J 93 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL J 94 " --> pdb=" O ALA J 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 90 through 94' Processing helix chain 'J' and resid 98 through 103 Processing helix chain 'J' and resid 103 through 111 removed outlier: 3.582A pdb=" N PHE J 107 " --> pdb=" O TYR J 103 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU J 108 " --> pdb=" O TYR J 104 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS J 109 " --> pdb=" O SER J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.692A pdb=" N ILE J 118 " --> pdb=" O THR J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 158 removed outlier: 3.531A pdb=" N GLY J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE J 156 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 178 removed outlier: 3.910A pdb=" N LYS J 175 " --> pdb=" O ASP J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 213 removed outlier: 3.653A pdb=" N LYS J 205 " --> pdb=" O SER J 201 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN J 208 " --> pdb=" O THR J 204 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP J 210 " --> pdb=" O GLU J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 222 removed outlier: 3.635A pdb=" N ILE J 217 " --> pdb=" O GLU J 213 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE J 222 " --> pdb=" O GLU J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.719A pdb=" N MET J 232 " --> pdb=" O SER J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 240 removed outlier: 3.847A pdb=" N LEU J 239 " --> pdb=" O LYS J 235 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 473 through 475 removed outlier: 3.632A pdb=" N ASP G 475 " --> pdb=" O ALA G 480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 497 through 498 removed outlier: 3.505A pdb=" N SER G 497 " --> pdb=" O TYR G 504 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 37 through 39 removed outlier: 3.701A pdb=" N SER H 38 " --> pdb=" O HIS H 365 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS H 365 " --> pdb=" O SER H 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.619A pdb=" N SER H 81 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU H 69 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA H 79 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE H 71 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER H 77 " --> pdb=" O PHE H 71 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU H 87 " --> pdb=" O TYR H 104 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR H 104 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL H 89 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER H 100 " --> pdb=" O PHE H 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 128 through 131 removed outlier: 6.171A pdb=" N ILE H 137 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR H 154 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU H 139 " --> pdb=" O LEU H 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.650A pdb=" N THR H 165 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE H 184 " --> pdb=" O SER H 198 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER H 198 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU H 186 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 214 through 217 removed outlier: 3.638A pdb=" N SER H 214 " --> pdb=" O GLY H 227 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU H 233 " --> pdb=" O LYS H 248 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS H 248 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE H 235 " --> pdb=" O CYS H 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 256 through 261 removed outlier: 3.838A pdb=" N GLU H 258 " --> pdb=" O GLY H 271 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN H 276 " --> pdb=" O SER H 272 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS H 277 " --> pdb=" O ILE H 290 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ILE H 290 " --> pdb=" O CYS H 277 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL H 279 " --> pdb=" O GLU H 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 298 through 303 removed outlier: 3.519A pdb=" N THR H 300 " --> pdb=" O CYS H 313 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU H 310 " --> pdb=" O TYR H 322 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET H 318 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL H 319 " --> pdb=" O SER H 332 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER H 332 " --> pdb=" O VAL H 319 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE H 321 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 146 through 150 removed outlier: 3.738A pdb=" N ASP I 193 " --> pdb=" O THR I 146 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU I 148 " --> pdb=" O ILE I 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE I 191 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL I 150 " --> pdb=" O TYR I 189 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 2121 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.27 Time building geometry restraints manager: 6.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6867 1.34 - 1.46: 4164 1.46 - 1.58: 10870 1.58 - 1.70: 0 1.70 - 1.82: 141 Bond restraints: 22042 Sorted by residual: bond pdb=" C SER G 22 " pdb=" N PRO G 23 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.66e+01 bond pdb=" N ARG G 35 " pdb=" CA ARG G 35 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.24e+00 bond pdb=" C PHE G1155 " pdb=" N PRO G1156 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.31e+00 bond pdb=" C ILE G 418 " pdb=" N PRO G 419 " ideal model delta sigma weight residual 1.337 1.363 -0.027 1.11e-02 8.12e+03 5.87e+00 bond pdb=" C THR G 900 " pdb=" N PRO G 901 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.23e-02 6.61e+03 5.49e+00 ... (remaining 22037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 29171 2.98 - 5.97: 520 5.97 - 8.95: 71 8.95 - 11.93: 6 11.93 - 14.91: 2 Bond angle restraints: 29770 Sorted by residual: angle pdb=" N ILE G 478 " pdb=" CA ILE G 478 " pdb=" C ILE G 478 " ideal model delta sigma weight residual 112.43 105.23 7.20 9.20e-01 1.18e+00 6.13e+01 angle pdb=" N ILE F 55 " pdb=" CA ILE F 55 " pdb=" C ILE F 55 " ideal model delta sigma weight residual 113.20 106.84 6.36 9.60e-01 1.09e+00 4.39e+01 angle pdb=" N VAL G 433 " pdb=" CA VAL G 433 " pdb=" C VAL G 433 " ideal model delta sigma weight residual 111.62 106.52 5.10 7.90e-01 1.60e+00 4.17e+01 angle pdb=" C PHE F 437 " pdb=" N GLU F 438 " pdb=" CA GLU F 438 " ideal model delta sigma weight residual 120.38 128.69 -8.31 1.37e+00 5.33e-01 3.68e+01 angle pdb=" C LYS F 171 " pdb=" N GLN F 172 " pdb=" CA GLN F 172 " ideal model delta sigma weight residual 120.58 128.12 -7.54 1.32e+00 5.74e-01 3.27e+01 ... (remaining 29765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 11727 17.91 - 35.81: 1376 35.81 - 53.72: 263 53.72 - 71.62: 41 71.62 - 89.53: 26 Dihedral angle restraints: 13433 sinusoidal: 5539 harmonic: 7894 Sorted by residual: dihedral pdb=" CA LEU J 124 " pdb=" C LEU J 124 " pdb=" N SER J 125 " pdb=" CA SER J 125 " ideal model delta harmonic sigma weight residual 180.00 137.37 42.63 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA SER G 143 " pdb=" C SER G 143 " pdb=" N TRP G 144 " pdb=" CA TRP G 144 " ideal model delta harmonic sigma weight residual -180.00 -142.10 -37.90 0 5.00e+00 4.00e-02 5.74e+01 dihedral pdb=" CA ILE G 34 " pdb=" C ILE G 34 " pdb=" N ARG G 35 " pdb=" CA ARG G 35 " ideal model delta harmonic sigma weight residual -180.00 -143.50 -36.50 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 13430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2980 0.076 - 0.153: 328 0.153 - 0.229: 40 0.229 - 0.305: 4 0.305 - 0.381: 2 Chirality restraints: 3354 Sorted by residual: chirality pdb=" CB ILE H 354 " pdb=" CA ILE H 354 " pdb=" CG1 ILE H 354 " pdb=" CG2 ILE H 354 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB ILE F 168 " pdb=" CA ILE F 168 " pdb=" CG1 ILE F 168 " pdb=" CG2 ILE F 168 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB VAL J 90 " pdb=" CA VAL J 90 " pdb=" CG1 VAL J 90 " pdb=" CG2 VAL J 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 3351 not shown) Planarity restraints: 3771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F 141 " 0.060 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO F 142 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO F 142 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 142 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 432 " 0.038 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR G 432 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR G 432 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR G 432 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR G 432 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR G 432 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G 432 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 432 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 169 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO H 170 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 170 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 170 " 0.042 5.00e-02 4.00e+02 ... (remaining 3768 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6000 2.80 - 3.33: 18058 3.33 - 3.85: 32343 3.85 - 4.38: 39218 4.38 - 4.90: 66859 Nonbonded interactions: 162478 Sorted by model distance: nonbonded pdb=" O ASP G 943 " pdb=" OG1 THR G 947 " model vdw 2.276 3.040 nonbonded pdb=" OG SER I 47 " pdb=" OD2 ASP I 49 " model vdw 2.322 3.040 nonbonded pdb=" OD1 ASN G 794 " pdb=" OG SER G1044 " model vdw 2.328 3.040 nonbonded pdb=" O SER F 247 " pdb=" OG SER F 247 " model vdw 2.329 3.040 nonbonded pdb=" OG SER F 211 " pdb=" NZ LYS G 171 " model vdw 2.335 3.120 ... (remaining 162473 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=0.38 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: 395.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 55.970 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.190 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: 0.030 Load rotamer database and sin/cos tables:3.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 456.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.006 0.069 22042 Z= 0.280 Angle : 1.084 14.914 29770 Z= 0.655 Chirality : 0.052 0.381 3354 Planarity : 0.007 0.091 3771 Dihedral : 15.893 89.528 8289 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.05 % Favored : 92.87 % Rotamer: Outliers : 0.24 % Allowed : 7.47 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -6.70 (0.09), residues: 2637 helix: -4.79 (0.04), residues: 1510 sheet: -2.46 (0.35), residues: 164 loop : -3.86 (0.14), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 238 HIS 0.009 0.001 HIS H 365 PHE 0.025 0.002 PHE H 268 TYR 0.053 0.002 TYR G 432 ARG 0.010 0.001 ARG J 185 Details of bonding type rmsd hydrogen bonds : bond 0.36550 ( 716) hydrogen bonds : angle 9.97108 ( 2121) covalent geometry : bond 0.00617 (22042) covalent geometry : angle 1.08352 (29770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 322 time to evaluate : 4.097 Fit side-chains revert: symmetry clash REVERT: F 66 ASP cc_start: 0.7079 (t0) cc_final: 0.6762 (t0) REVERT: F 237 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6393 (tp30) REVERT: F 253 VAL cc_start: 0.8591 (m) cc_final: 0.8353 (p) REVERT: F 341 HIS cc_start: 0.7579 (m-70) cc_final: 0.7298 (m90) REVERT: G 221 ILE cc_start: 0.8362 (mt) cc_final: 0.8091 (mt) REVERT: G 1063 MET cc_start: 0.8233 (mmt) cc_final: 0.8004 (mmt) REVERT: H 65 GLU cc_start: 0.7171 (pt0) cc_final: 0.6946 (pt0) REVERT: I 152 ARG cc_start: 0.7883 (ttm170) cc_final: 0.7427 (ptt-90) REVERT: I 192 TYR cc_start: 0.7789 (t80) cc_final: 0.7496 (t80) REVERT: J 232 MET cc_start: 0.0733 (mmm) cc_final: -0.0535 (ttt) outliers start: 6 outliers final: 0 residues processed: 327 average time/residue: 0.4291 time to fit residues: 212.6266 Evaluate side-chains 193 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 110 optimal weight: 0.0770 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 206 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 238 optimal weight: 0.0370 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 54 ASN F 95 ASN F 190 ASN F 221 ASN F 397 GLN F 444 ASN G 4 GLN G 54 ASN G 78 ASN G 136 HIS G 318 ASN G 492 HIS ** G 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 615 ASN G 703 GLN G 718 GLN G 749 ASN G 786 ASN G 794 ASN G 801 GLN G 916 ASN G 984 HIS G1215 GLN G1239 GLN ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 ASN H 223 HIS H 359 ASN I 10 GLN I 76 GLN I 114 HIS J 29 ASN J 74 GLN J 119 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.155928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114592 restraints weight = 32699.605| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.60 r_work: 0.3283 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22042 Z= 0.121 Angle : 0.594 10.854 29770 Z= 0.315 Chirality : 0.040 0.186 3354 Planarity : 0.005 0.070 3771 Dihedral : 5.734 29.331 2857 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.71 % Favored : 93.25 % Rotamer: Outliers : 1.38 % Allowed : 11.69 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -5.22 (0.12), residues: 2637 helix: -3.37 (0.09), residues: 1543 sheet: -1.88 (0.36), residues: 167 loop : -3.63 (0.15), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 227 HIS 0.005 0.001 HIS F 265 PHE 0.026 0.001 PHE G 325 TYR 0.017 0.001 TYR F 325 ARG 0.007 0.000 ARG G 473 Details of bonding type rmsd hydrogen bonds : bond 0.05654 ( 716) hydrogen bonds : angle 4.74470 ( 2121) covalent geometry : bond 0.00248 (22042) covalent geometry : angle 0.59394 (29770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 190 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8047 (t0) REVERT: F 207 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7452 (tm-30) REVERT: F 237 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6471 (tp30) REVERT: F 253 VAL cc_start: 0.8592 (m) cc_final: 0.8320 (p) REVERT: F 300 GLU cc_start: 0.8175 (tp30) cc_final: 0.7937 (tp30) REVERT: F 325 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.5746 (p90) REVERT: F 341 HIS cc_start: 0.8059 (m-70) cc_final: 0.7732 (m90) REVERT: G 1 MET cc_start: 0.6597 (ppp) cc_final: 0.4790 (tmm) REVERT: G 617 MET cc_start: 0.8707 (tpp) cc_final: 0.8344 (tpp) REVERT: G 624 ASP cc_start: 0.6441 (m-30) cc_final: 0.6214 (m-30) REVERT: G 1139 MET cc_start: 0.6837 (mmp) cc_final: 0.6418 (mmp) REVERT: H 65 GLU cc_start: 0.7480 (pt0) cc_final: 0.7196 (pt0) REVERT: H 102 GLU cc_start: 0.5399 (OUTLIER) cc_final: 0.5164 (mt-10) REVERT: I 16 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8383 (t-170) REVERT: I 219 GLU cc_start: 0.8226 (tt0) cc_final: 0.7962 (tt0) REVERT: J 119 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8375 (t0) REVERT: J 232 MET cc_start: 0.0105 (mmm) cc_final: -0.0733 (ttt) outliers start: 34 outliers final: 10 residues processed: 263 average time/residue: 0.3443 time to fit residues: 141.5886 Evaluate side-chains 211 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain G residue 649 ASP Chi-restraints excluded: chain G residue 763 ILE Chi-restraints excluded: chain G residue 842 ASN Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 194 optimal weight: 0.6980 chunk 251 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 208 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 365 HIS H 372 ASN J 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.153400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111889 restraints weight = 32205.723| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.53 r_work: 0.3231 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22042 Z= 0.138 Angle : 0.570 10.744 29770 Z= 0.298 Chirality : 0.041 0.232 3354 Planarity : 0.004 0.063 3771 Dihedral : 5.290 26.658 2857 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.41 % Favored : 93.55 % Rotamer: Outliers : 2.11 % Allowed : 14.21 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -4.13 (0.13), residues: 2637 helix: -2.33 (0.11), residues: 1567 sheet: -1.66 (0.36), residues: 168 loop : -3.44 (0.16), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 280 HIS 0.006 0.001 HIS G 211 PHE 0.023 0.001 PHE G1147 TYR 0.018 0.001 TYR G 432 ARG 0.005 0.000 ARG G1142 Details of bonding type rmsd hydrogen bonds : bond 0.05095 ( 716) hydrogen bonds : angle 4.20383 ( 2121) covalent geometry : bond 0.00320 (22042) covalent geometry : angle 0.56951 (29770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 207 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7644 (tm-30) REVERT: F 300 GLU cc_start: 0.8266 (tp30) cc_final: 0.7814 (tp30) REVERT: F 325 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.5798 (p90) REVERT: F 341 HIS cc_start: 0.8036 (m-70) cc_final: 0.7804 (m90) REVERT: G 177 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: G 435 GLU cc_start: 0.7928 (pm20) cc_final: 0.7676 (mp0) REVERT: H 65 GLU cc_start: 0.7560 (pt0) cc_final: 0.7341 (pt0) REVERT: H 102 GLU cc_start: 0.5454 (OUTLIER) cc_final: 0.5249 (mt-10) REVERT: I 46 LEU cc_start: 0.8376 (pt) cc_final: 0.7877 (mm) REVERT: I 165 LYS cc_start: 0.8452 (tptp) cc_final: 0.8178 (mmpt) REVERT: I 219 GLU cc_start: 0.8152 (tt0) cc_final: 0.7836 (tt0) REVERT: J 232 MET cc_start: 0.0086 (mmm) cc_final: -0.0783 (ttt) outliers start: 52 outliers final: 27 residues processed: 249 average time/residue: 0.3299 time to fit residues: 131.5974 Evaluate side-chains 218 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 265 HIS Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 432 TYR Chi-restraints excluded: chain G residue 649 ASP Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 975 THR Chi-restraints excluded: chain G residue 1027 ILE Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1068 THR Chi-restraints excluded: chain G residue 1078 LEU Chi-restraints excluded: chain G residue 1150 HIS Chi-restraints excluded: chain G residue 1162 ILE Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 167 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 202 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 ASN F 199 HIS G1113 GLN ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.152934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111360 restraints weight = 33657.680| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.47 r_work: 0.3223 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22042 Z= 0.153 Angle : 0.567 10.669 29770 Z= 0.295 Chirality : 0.042 0.174 3354 Planarity : 0.003 0.055 3771 Dihedral : 5.151 27.318 2857 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.60 % Favored : 93.36 % Rotamer: Outliers : 2.40 % Allowed : 16.28 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -3.51 (0.14), residues: 2637 helix: -1.77 (0.12), residues: 1570 sheet: -1.44 (0.35), residues: 179 loop : -3.34 (0.16), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 280 HIS 0.005 0.001 HIS G 211 PHE 0.022 0.001 PHE G1147 TYR 0.019 0.001 TYR F 325 ARG 0.003 0.000 ARG G1002 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 716) hydrogen bonds : angle 4.05301 ( 2121) covalent geometry : bond 0.00363 (22042) covalent geometry : angle 0.56658 (29770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: F 190 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.8012 (t0) REVERT: F 207 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7936 (tm-30) REVERT: F 325 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.6014 (p90) REVERT: G 1 MET cc_start: 0.6611 (ppp) cc_final: 0.4741 (tmm) REVERT: G 177 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: G 325 PHE cc_start: 0.8652 (t80) cc_final: 0.8277 (t80) REVERT: G 435 GLU cc_start: 0.8201 (pm20) cc_final: 0.7953 (mp0) REVERT: H 65 GLU cc_start: 0.7851 (pt0) cc_final: 0.7639 (pt0) REVERT: H 102 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.5655 (mt-10) REVERT: I 46 LEU cc_start: 0.8396 (pt) cc_final: 0.7822 (mm) REVERT: I 53 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6578 (tp) REVERT: I 165 LYS cc_start: 0.8613 (tptp) cc_final: 0.7801 (mtmt) REVERT: I 219 GLU cc_start: 0.8141 (tt0) cc_final: 0.7874 (tt0) REVERT: J 133 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6983 (mt-10) REVERT: J 232 MET cc_start: -0.0025 (mmm) cc_final: -0.1023 (ttt) REVERT: J 234 GLN cc_start: 0.3887 (OUTLIER) cc_final: 0.3515 (pm20) outliers start: 59 outliers final: 34 residues processed: 235 average time/residue: 0.3536 time to fit residues: 133.0972 Evaluate side-chains 227 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 265 HIS Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 432 TYR Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 649 ASP Chi-restraints excluded: chain G residue 763 ILE Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 943 ASP Chi-restraints excluded: chain G residue 975 THR Chi-restraints excluded: chain G residue 1027 ILE Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1113 GLN Chi-restraints excluded: chain G residue 1150 HIS Chi-restraints excluded: chain G residue 1162 ILE Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 313 CYS Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 234 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 180 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 19 optimal weight: 0.0370 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 ASN G 591 ASN G 744 ASN G1113 GLN ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111005 restraints weight = 33181.385| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.72 r_work: 0.3240 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22042 Z= 0.105 Angle : 0.509 10.223 29770 Z= 0.265 Chirality : 0.040 0.157 3354 Planarity : 0.003 0.051 3771 Dihedral : 4.795 25.755 2857 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.11 % Favored : 93.86 % Rotamer: Outliers : 2.11 % Allowed : 17.62 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -2.90 (0.15), residues: 2637 helix: -1.25 (0.13), residues: 1562 sheet: -1.26 (0.35), residues: 178 loop : -3.14 (0.17), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 280 HIS 0.004 0.001 HIS F 265 PHE 0.018 0.001 PHE G1147 TYR 0.017 0.001 TYR G 808 ARG 0.002 0.000 ARG G1002 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 716) hydrogen bonds : angle 3.73859 ( 2121) covalent geometry : bond 0.00238 (22042) covalent geometry : angle 0.50927 (29770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: F 325 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.5765 (p90) REVERT: F 522 LYS cc_start: 0.8844 (mttt) cc_final: 0.8417 (mptt) REVERT: G 177 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8086 (mm-30) REVERT: G 325 PHE cc_start: 0.8578 (t80) cc_final: 0.8234 (t80) REVERT: G 617 MET cc_start: 0.8638 (tpt) cc_final: 0.8347 (tpp) REVERT: G 726 MET cc_start: 0.8059 (mmp) cc_final: 0.7851 (mtm) REVERT: G 1063 MET cc_start: 0.7911 (mmp) cc_final: 0.7708 (mmp) REVERT: G 1120 GLU cc_start: 0.8275 (tt0) cc_final: 0.8045 (tm-30) REVERT: H 51 ARG cc_start: 0.5997 (tpt170) cc_final: 0.5709 (mtp85) REVERT: H 389 ARG cc_start: 0.6291 (tpt170) cc_final: 0.5922 (ttm-80) REVERT: I 46 LEU cc_start: 0.8149 (pt) cc_final: 0.7706 (mm) REVERT: I 53 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6483 (tp) REVERT: I 165 LYS cc_start: 0.8582 (tptp) cc_final: 0.7772 (mtmt) REVERT: J 133 GLU cc_start: 0.7634 (mm-30) cc_final: 0.6997 (mt-10) REVERT: J 232 MET cc_start: -0.0051 (mmm) cc_final: -0.1019 (ttt) REVERT: J 234 GLN cc_start: 0.3970 (OUTLIER) cc_final: 0.3596 (pm20) outliers start: 52 outliers final: 31 residues processed: 246 average time/residue: 0.3624 time to fit residues: 141.9368 Evaluate side-chains 222 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 432 TYR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 649 ASP Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 943 ASP Chi-restraints excluded: chain G residue 975 THR Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1078 LEU Chi-restraints excluded: chain G residue 1162 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 313 CYS Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 234 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 158 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1113 GLN ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.154391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113132 restraints weight = 32627.808| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.52 r_work: 0.3251 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22042 Z= 0.105 Angle : 0.510 10.035 29770 Z= 0.264 Chirality : 0.040 0.154 3354 Planarity : 0.003 0.048 3771 Dihedral : 4.632 25.328 2857 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 2.27 % Allowed : 18.51 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -2.51 (0.15), residues: 2637 helix: -0.92 (0.13), residues: 1569 sheet: -1.18 (0.35), residues: 178 loop : -3.01 (0.18), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 280 HIS 0.005 0.001 HIS F 265 PHE 0.021 0.001 PHE G1147 TYR 0.014 0.001 TYR G 808 ARG 0.002 0.000 ARG J 59 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 716) hydrogen bonds : angle 3.63555 ( 2121) covalent geometry : bond 0.00239 (22042) covalent geometry : angle 0.50961 (29770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: F 325 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.5466 (p90) REVERT: F 522 LYS cc_start: 0.8922 (mttt) cc_final: 0.8425 (mptt) REVERT: G 1 MET cc_start: 0.6785 (ppp) cc_final: 0.4744 (tmm) REVERT: G 177 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8101 (mm-30) REVERT: G 325 PHE cc_start: 0.8582 (t80) cc_final: 0.8246 (t80) REVERT: G 617 MET cc_start: 0.8842 (tpt) cc_final: 0.8573 (tpp) REVERT: G 726 MET cc_start: 0.8469 (mmp) cc_final: 0.8043 (mtm) REVERT: G 1120 GLU cc_start: 0.8271 (tt0) cc_final: 0.7975 (tm-30) REVERT: H 51 ARG cc_start: 0.5821 (tpt170) cc_final: 0.5525 (mtp85) REVERT: H 389 ARG cc_start: 0.6162 (tpt170) cc_final: 0.5827 (ttm-80) REVERT: I 46 LEU cc_start: 0.8179 (pt) cc_final: 0.7635 (mm) REVERT: I 53 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6469 (tp) REVERT: I 99 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7410 (ptmt) REVERT: I 165 LYS cc_start: 0.8630 (tptp) cc_final: 0.7747 (mtmt) REVERT: J 133 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7043 (mt-10) REVERT: J 232 MET cc_start: -0.0040 (mmm) cc_final: -0.1116 (ttt) REVERT: J 234 GLN cc_start: 0.3870 (OUTLIER) cc_final: 0.3561 (pm20) outliers start: 56 outliers final: 41 residues processed: 228 average time/residue: 0.3587 time to fit residues: 133.5527 Evaluate side-chains 224 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 265 HIS Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 597 VAL Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 432 TYR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 625 ILE Chi-restraints excluded: chain G residue 649 ASP Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 937 LEU Chi-restraints excluded: chain G residue 943 ASP Chi-restraints excluded: chain G residue 975 THR Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1078 LEU Chi-restraints excluded: chain G residue 1113 GLN Chi-restraints excluded: chain G residue 1162 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 354 ILE Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 234 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 38 optimal weight: 1.9990 chunk 215 optimal weight: 0.4980 chunk 211 optimal weight: 0.0010 chunk 89 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1113 GLN ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.152153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110729 restraints weight = 33327.443| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.45 r_work: 0.3206 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22042 Z= 0.152 Angle : 0.558 9.861 29770 Z= 0.288 Chirality : 0.042 0.166 3354 Planarity : 0.003 0.046 3771 Dihedral : 4.863 27.386 2857 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.48 % Favored : 93.48 % Rotamer: Outliers : 2.72 % Allowed : 18.31 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -2.34 (0.16), residues: 2637 helix: -0.82 (0.13), residues: 1564 sheet: -1.19 (0.36), residues: 178 loop : -2.83 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 280 HIS 0.006 0.001 HIS G 211 PHE 0.015 0.001 PHE G 518 TYR 0.019 0.001 TYR G 432 ARG 0.004 0.000 ARG G1116 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 716) hydrogen bonds : angle 3.78261 ( 2121) covalent geometry : bond 0.00363 (22042) covalent geometry : angle 0.55821 (29770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 183 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: F 325 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.5736 (p90) REVERT: F 495 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: F 522 LYS cc_start: 0.8951 (mttt) cc_final: 0.8454 (mptt) REVERT: F 594 PHE cc_start: 0.4784 (OUTLIER) cc_final: 0.4538 (m-10) REVERT: F 599 GLU cc_start: 0.4986 (OUTLIER) cc_final: 0.3989 (pp20) REVERT: G 177 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: G 325 PHE cc_start: 0.8649 (t80) cc_final: 0.8315 (t80) REVERT: G 398 ASP cc_start: 0.8272 (m-30) cc_final: 0.7931 (m-30) REVERT: G 580 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8270 (p90) REVERT: G 617 MET cc_start: 0.8853 (tpt) cc_final: 0.8597 (tpp) REVERT: G 957 HIS cc_start: 0.7278 (t70) cc_final: 0.6955 (t-90) REVERT: H 51 ARG cc_start: 0.5836 (tpt170) cc_final: 0.5448 (mtp85) REVERT: H 389 ARG cc_start: 0.6333 (tpt170) cc_final: 0.6010 (ttm-80) REVERT: I 46 LEU cc_start: 0.8097 (pt) cc_final: 0.7562 (mm) REVERT: I 53 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6544 (tp) REVERT: I 165 LYS cc_start: 0.8639 (tptp) cc_final: 0.7737 (mtmt) REVERT: J 133 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7126 (mt-10) REVERT: J 229 MET cc_start: 0.1153 (mmt) cc_final: -0.0063 (ttm) REVERT: J 232 MET cc_start: 0.0217 (mmm) cc_final: -0.0903 (ttt) REVERT: J 234 GLN cc_start: 0.3765 (OUTLIER) cc_final: 0.3498 (pm20) outliers start: 67 outliers final: 44 residues processed: 235 average time/residue: 0.3063 time to fit residues: 116.8280 Evaluate side-chains 233 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 265 HIS Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 594 PHE Chi-restraints excluded: chain F residue 597 VAL Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 432 TYR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 580 PHE Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 625 ILE Chi-restraints excluded: chain G residue 649 ASP Chi-restraints excluded: chain G residue 763 ILE Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 937 LEU Chi-restraints excluded: chain G residue 943 ASP Chi-restraints excluded: chain G residue 975 THR Chi-restraints excluded: chain G residue 1027 ILE Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1078 LEU Chi-restraints excluded: chain G residue 1113 GLN Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 354 ILE Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 234 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 155 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 239 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 243 optimal weight: 0.0570 chunk 176 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.152606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.109937 restraints weight = 33399.653| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.49 r_work: 0.3246 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22042 Z= 0.116 Angle : 0.535 9.939 29770 Z= 0.273 Chirality : 0.041 0.199 3354 Planarity : 0.003 0.045 3771 Dihedral : 4.669 25.845 2857 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.22 % Favored : 93.74 % Rotamer: Outliers : 2.56 % Allowed : 18.76 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -2.09 (0.16), residues: 2637 helix: -0.58 (0.13), residues: 1562 sheet: -1.11 (0.36), residues: 178 loop : -2.80 (0.18), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 280 HIS 0.004 0.001 HIS F 265 PHE 0.013 0.001 PHE G 518 TYR 0.015 0.001 TYR G 808 ARG 0.002 0.000 ARG I 229 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 716) hydrogen bonds : angle 3.62914 ( 2121) covalent geometry : bond 0.00271 (22042) covalent geometry : angle 0.53505 (29770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 186 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: F 325 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.5476 (p90) REVERT: F 495 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: F 522 LYS cc_start: 0.8981 (mttt) cc_final: 0.8531 (mptt) REVERT: F 594 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.4578 (m-10) REVERT: F 599 GLU cc_start: 0.4991 (OUTLIER) cc_final: 0.4025 (pp20) REVERT: G 17 VAL cc_start: 0.5686 (OUTLIER) cc_final: 0.5443 (t) REVERT: G 177 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: G 325 PHE cc_start: 0.8728 (t80) cc_final: 0.8378 (t80) REVERT: G 334 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: G 580 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8209 (p90) REVERT: G 617 MET cc_start: 0.8847 (tpt) cc_final: 0.8610 (tpp) REVERT: G 726 MET cc_start: 0.8234 (mmp) cc_final: 0.7966 (mtm) REVERT: G 1062 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6576 (tt) REVERT: G 1120 GLU cc_start: 0.8260 (tt0) cc_final: 0.8035 (tm-30) REVERT: H 51 ARG cc_start: 0.5856 (tpt170) cc_final: 0.5494 (mtp85) REVERT: H 389 ARG cc_start: 0.6432 (tpt170) cc_final: 0.6109 (ttm-80) REVERT: I 46 LEU cc_start: 0.8057 (pt) cc_final: 0.7452 (mm) REVERT: I 53 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6445 (tp) REVERT: I 99 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7793 (ptmt) REVERT: I 165 LYS cc_start: 0.8618 (tptp) cc_final: 0.7725 (mtmt) REVERT: I 219 GLU cc_start: 0.7889 (tt0) cc_final: 0.7609 (tt0) REVERT: J 133 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7133 (mt-10) REVERT: J 229 MET cc_start: 0.1206 (mmt) cc_final: -0.0127 (ttm) REVERT: J 232 MET cc_start: 0.0275 (mmm) cc_final: -0.1002 (ttt) REVERT: J 234 GLN cc_start: 0.3570 (OUTLIER) cc_final: 0.3331 (pm20) outliers start: 63 outliers final: 43 residues processed: 233 average time/residue: 0.3089 time to fit residues: 117.6272 Evaluate side-chains 236 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 265 HIS Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 594 PHE Chi-restraints excluded: chain F residue 597 VAL Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 432 TYR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 580 PHE Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 625 ILE Chi-restraints excluded: chain G residue 649 ASP Chi-restraints excluded: chain G residue 763 ILE Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 937 LEU Chi-restraints excluded: chain G residue 943 ASP Chi-restraints excluded: chain G residue 975 THR Chi-restraints excluded: chain G residue 1027 ILE Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1062 LEU Chi-restraints excluded: chain G residue 1078 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 354 ILE Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 234 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 145 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.0050 chunk 201 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1113 GLN ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.154439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112095 restraints weight = 32986.450| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.71 r_work: 0.3254 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22042 Z= 0.101 Angle : 0.516 9.829 29770 Z= 0.262 Chirality : 0.040 0.166 3354 Planarity : 0.003 0.044 3771 Dihedral : 4.433 23.900 2857 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.99 % Favored : 93.97 % Rotamer: Outliers : 2.23 % Allowed : 19.33 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2637 helix: -0.31 (0.14), residues: 1557 sheet: -1.05 (0.38), residues: 168 loop : -2.71 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 90 HIS 0.005 0.001 HIS F 265 PHE 0.014 0.001 PHE G 89 TYR 0.014 0.001 TYR G 808 ARG 0.002 0.000 ARG F 147 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 716) hydrogen bonds : angle 3.47230 ( 2121) covalent geometry : bond 0.00232 (22042) covalent geometry : angle 0.51562 (29770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: F 325 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.5089 (p90) REVERT: F 373 ASP cc_start: 0.8596 (t0) cc_final: 0.8333 (t0) REVERT: F 495 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (mp0) REVERT: F 522 LYS cc_start: 0.8916 (mttt) cc_final: 0.8525 (mptt) REVERT: F 594 PHE cc_start: 0.4729 (OUTLIER) cc_final: 0.4396 (m-10) REVERT: G 1 MET cc_start: 0.6466 (ppp) cc_final: 0.4811 (ttp) REVERT: G 17 VAL cc_start: 0.5452 (OUTLIER) cc_final: 0.5252 (t) REVERT: G 177 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8052 (mm-30) REVERT: G 325 PHE cc_start: 0.8582 (t80) cc_final: 0.8256 (t80) REVERT: G 580 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8004 (p90) REVERT: G 617 MET cc_start: 0.8552 (tpt) cc_final: 0.8318 (tpp) REVERT: G 1062 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6552 (tt) REVERT: G 1120 GLU cc_start: 0.8290 (tt0) cc_final: 0.8006 (tm-30) REVERT: G 1191 HIS cc_start: 0.7635 (m90) cc_final: 0.7376 (m90) REVERT: H 51 ARG cc_start: 0.5848 (tpt170) cc_final: 0.5569 (mtp85) REVERT: H 97 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6113 (t80) REVERT: H 182 GLU cc_start: 0.7623 (tt0) cc_final: 0.7296 (tt0) REVERT: H 389 ARG cc_start: 0.6259 (tpt170) cc_final: 0.5980 (ttm-80) REVERT: I 165 LYS cc_start: 0.8559 (tptp) cc_final: 0.7742 (mtmt) REVERT: J 133 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7050 (mt-10) REVERT: J 232 MET cc_start: 0.0045 (mmm) cc_final: -0.1174 (ttm) outliers start: 55 outliers final: 34 residues processed: 236 average time/residue: 0.3107 time to fit residues: 118.6521 Evaluate side-chains 226 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 594 PHE Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 432 TYR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 580 PHE Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 625 ILE Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 937 LEU Chi-restraints excluded: chain G residue 943 ASP Chi-restraints excluded: chain G residue 975 THR Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1062 LEU Chi-restraints excluded: chain G residue 1078 LEU Chi-restraints excluded: chain G residue 1113 GLN Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 354 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 250 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 180 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 HIS G1113 GLN ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.152001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109141 restraints weight = 33277.219| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.68 r_work: 0.3209 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22042 Z= 0.149 Angle : 0.570 11.341 29770 Z= 0.288 Chirality : 0.042 0.194 3354 Planarity : 0.003 0.044 3771 Dihedral : 4.657 24.720 2857 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 2.23 % Allowed : 19.41 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2637 helix: -0.40 (0.13), residues: 1564 sheet: -1.02 (0.38), residues: 167 loop : -2.68 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 280 HIS 0.005 0.001 HIS G 211 PHE 0.016 0.001 PHE G 518 TYR 0.019 0.001 TYR G 432 ARG 0.006 0.000 ARG J 88 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 716) hydrogen bonds : angle 3.64232 ( 2121) covalent geometry : bond 0.00355 (22042) covalent geometry : angle 0.57041 (29770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: F 325 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.5190 (p90) REVERT: F 495 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: F 522 LYS cc_start: 0.8932 (mttt) cc_final: 0.8530 (mptt) REVERT: F 594 PHE cc_start: 0.4658 (OUTLIER) cc_final: 0.4314 (m-10) REVERT: F 599 GLU cc_start: 0.4987 (OUTLIER) cc_final: 0.4057 (pp20) REVERT: G 1 MET cc_start: 0.6642 (ppp) cc_final: 0.5093 (ttp) REVERT: G 177 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: G 325 PHE cc_start: 0.8640 (t80) cc_final: 0.8312 (t80) REVERT: G 398 ASP cc_start: 0.8236 (m-30) cc_final: 0.7901 (m-30) REVERT: G 580 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8191 (p90) REVERT: G 617 MET cc_start: 0.8549 (tpt) cc_final: 0.8323 (tpp) REVERT: G 957 HIS cc_start: 0.7131 (t70) cc_final: 0.6877 (t-90) REVERT: G 1062 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6511 (tt) REVERT: G 1191 HIS cc_start: 0.7658 (m90) cc_final: 0.7394 (m90) REVERT: H 51 ARG cc_start: 0.5859 (tpt170) cc_final: 0.5501 (mtp85) REVERT: H 97 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.5750 (t80) REVERT: H 182 GLU cc_start: 0.7632 (tt0) cc_final: 0.7310 (tt0) REVERT: H 389 ARG cc_start: 0.6280 (tpt170) cc_final: 0.5972 (ttm-80) REVERT: I 219 GLU cc_start: 0.7828 (tt0) cc_final: 0.7532 (tt0) REVERT: J 133 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7218 (mt-10) REVERT: J 151 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: J 229 MET cc_start: 0.1133 (mmt) cc_final: -0.0124 (ttm) REVERT: J 232 MET cc_start: -0.0278 (mmm) cc_final: -0.1075 (ttm) outliers start: 55 outliers final: 42 residues processed: 228 average time/residue: 0.3070 time to fit residues: 113.5696 Evaluate side-chains 231 residues out of total 2465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 265 HIS Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 594 PHE Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 432 TYR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 580 PHE Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 625 ILE Chi-restraints excluded: chain G residue 649 ASP Chi-restraints excluded: chain G residue 843 LEU Chi-restraints excluded: chain G residue 937 LEU Chi-restraints excluded: chain G residue 943 ASP Chi-restraints excluded: chain G residue 975 THR Chi-restraints excluded: chain G residue 1027 ILE Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1062 LEU Chi-restraints excluded: chain G residue 1078 LEU Chi-restraints excluded: chain G residue 1113 GLN Chi-restraints excluded: chain G residue 1162 ILE Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 354 ILE Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain J residue 167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 215 optimal weight: 0.8980 chunk 172 optimal weight: 0.0030 chunk 37 optimal weight: 0.0670 chunk 79 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 94 optimal weight: 0.0670 chunk 198 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.3466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.152218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109387 restraints weight = 33086.866| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.66 r_work: 0.3217 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 22042 Z= 0.159 Angle : 0.841 59.200 29770 Z= 0.500 Chirality : 0.044 0.650 3354 Planarity : 0.003 0.069 3771 Dihedral : 4.723 43.264 2857 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.26 % Favored : 93.67 % Rotamer: Outliers : 2.31 % Allowed : 19.33 % Favored : 78.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.16), residues: 2637 helix: -0.37 (0.13), residues: 1564 sheet: -1.03 (0.38), residues: 167 loop : -2.67 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 280 HIS 0.094 0.002 HIS F 59 PHE 0.015 0.001 PHE I 234 TYR 0.019 0.001 TYR G 432 ARG 0.005 0.000 ARG J 88 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 716) hydrogen bonds : angle 3.63886 ( 2121) covalent geometry : bond 0.00310 (22042) covalent geometry : angle 0.84059 (29770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15043.92 seconds wall clock time: 261 minutes 49.29 seconds (15709.29 seconds total)