Starting phenix.real_space_refine on Sun Sep 29 06:25:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2w_31669/09_2024/7v2w_31669.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2w_31669/09_2024/7v2w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2w_31669/09_2024/7v2w_31669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2w_31669/09_2024/7v2w_31669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2w_31669/09_2024/7v2w_31669.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2w_31669/09_2024/7v2w_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-5461/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: 12.35, per 1000 atoms: 0.57 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: 4.28 Conformation dependent library (CDL) restraints added in 2.7 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: 2.42 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: 6.56 Time building geometry restraints manager: 5.18 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: 23.850 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: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 44.830 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.050 ------------------------------------------------------------------------------- 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= 0.389 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 322 time to evaluate : 2.520 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: 0.3780 time to fit residues: 184.3364 Evaluate side-chains 193 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.425 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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= 0.158 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 *********************** 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 fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 190 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7771 (t0) REVERT: F 237 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6498 (tp30) REVERT: F 253 VAL cc_start: 0.8595 (m) cc_final: 0.8294 (p) REVERT: F 300 GLU cc_start: 0.7447 (tp30) cc_final: 0.7200 (tp30) REVERT: F 325 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.5574 (p90) REVERT: F 341 HIS cc_start: 0.7720 (m-70) cc_final: 0.7458 (m90) REVERT: G 1 MET cc_start: 0.6207 (ppp) cc_final: 0.4421 (tmm) REVERT: G 617 MET cc_start: 0.8428 (tpp) cc_final: 0.8004 (tpp) REVERT: G 1139 MET cc_start: 0.7052 (mmp) cc_final: 0.6651 (mmp) REVERT: H 65 GLU cc_start: 0.7133 (pt0) cc_final: 0.6923 (pt0) REVERT: H 102 GLU cc_start: 0.5185 (OUTLIER) cc_final: 0.4953 (mt-10) REVERT: I 219 GLU cc_start: 0.8221 (tt0) cc_final: 0.7974 (tt0) REVERT: J 119 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (t0) REVERT: J 232 MET cc_start: 0.0805 (mmm) cc_final: -0.0518 (ttt) outliers start: 34 outliers final: 10 residues processed: 263 average time/residue: 0.3322 time to fit residues: 136.7083 Evaluate side-chains 209 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 2.423 ------------------------------------------------------------------------------- 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 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 132 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 239 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 HIS ** 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 J 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2560 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= 0.267 Angle : 0.605 10.779 29770 Z= 0.316 Chirality : 0.043 0.218 3354 Planarity : 0.004 0.062 3771 Dihedral : 5.502 28.054 2857 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.67 % Favored : 93.25 % Rotamer: Outliers : 2.23 % Allowed : 14.21 % Favored : 83.56 % 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: -4.22 (0.13), residues: 2637 helix: -2.40 (0.11), residues: 1565 sheet: -1.74 (0.36), residues: 168 loop : -3.49 (0.16), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 280 HIS 0.008 0.001 HIS G 211 PHE 0.024 0.002 PHE G 518 TYR 0.021 0.001 TYR G 432 ARG 0.005 0.000 ARG G1142 *********************** 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 261 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 206 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 253 VAL cc_start: 0.8637 (m) cc_final: 0.8350 (p) REVERT: F 300 GLU cc_start: 0.7616 (tp30) cc_final: 0.7255 (tp30) REVERT: F 325 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.5763 (p90) REVERT: F 341 HIS cc_start: 0.7738 (m-70) cc_final: 0.7523 (m90) REVERT: G 177 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: G 1002 ARG cc_start: 0.8043 (ptp-110) cc_final: 0.7677 (ptp90) REVERT: H 102 GLU cc_start: 0.5343 (OUTLIER) cc_final: 0.5099 (mt-10) REVERT: H 365 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7692 (p90) REVERT: I 46 LEU cc_start: 0.8068 (pt) cc_final: 0.7680 (mm) REVERT: I 219 GLU cc_start: 0.8135 (tt0) cc_final: 0.7842 (tt0) REVERT: J 119 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8233 (t0) REVERT: J 232 MET cc_start: 0.0786 (mmm) cc_final: -0.0547 (ttt) outliers start: 55 outliers final: 30 residues processed: 243 average time/residue: 0.3296 time to fit residues: 128.6788 Evaluate side-chains 219 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 H residue 365 HIS 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 119 ASN 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 236 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1113 GLN ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 HIS H 365 HIS J 79 GLN J 119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22042 Z= 0.328 Angle : 0.626 10.668 29770 Z= 0.326 Chirality : 0.044 0.192 3354 Planarity : 0.004 0.053 3771 Dihedral : 5.512 29.683 2857 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 2.60 % Allowed : 16.73 % Favored : 80.67 % 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: -3.68 (0.14), residues: 2637 helix: -1.95 (0.12), residues: 1568 sheet: -1.60 (0.35), residues: 179 loop : -3.30 (0.17), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 280 HIS 0.018 0.001 HIS H 365 PHE 0.022 0.002 PHE G 518 TYR 0.023 0.002 TYR G 432 ARG 0.003 0.000 ARG G 484 *********************** 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 247 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 183 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: F 325 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6031 (p90) REVERT: F 341 HIS cc_start: 0.7678 (m-70) cc_final: 0.7445 (m90) REVERT: G 1 MET cc_start: 0.6315 (ppp) cc_final: 0.4477 (tmm) REVERT: G 177 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: G 398 ASP cc_start: 0.7937 (m-30) cc_final: 0.7593 (m-30) REVERT: G 452 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8225 (tp) REVERT: G 862 MET cc_start: 0.8278 (mmp) cc_final: 0.7898 (mmm) REVERT: H 102 GLU cc_start: 0.5424 (OUTLIER) cc_final: 0.5093 (mt-10) REVERT: H 365 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7512 (p90) REVERT: I 46 LEU cc_start: 0.8040 (pt) cc_final: 0.7655 (pp) REVERT: I 53 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6627 (tp) REVERT: I 219 GLU cc_start: 0.8125 (tt0) cc_final: 0.7843 (tt0) REVERT: J 191 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7376 (tm-30) REVERT: J 229 MET cc_start: 0.1830 (mmt) cc_final: 0.0335 (ttm) REVERT: J 232 MET cc_start: 0.0905 (mmm) cc_final: -0.0582 (ttt) REVERT: J 234 GLN cc_start: 0.4244 (OUTLIER) cc_final: 0.3729 (pm20) outliers start: 64 outliers final: 43 residues processed: 231 average time/residue: 0.3133 time to fit residues: 116.0097 Evaluate side-chains 231 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 180 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 188 LEU 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 337 VAL Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 470 ASP 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 213 MET 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 452 LEU Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 649 ASP Chi-restraints excluded: chain G residue 755 LEU 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 1068 THR 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 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 H residue 365 HIS 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 211 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 216 optimal weight: 0.0570 chunk 175 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 228 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 118 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 744 ASN ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** H 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 365 HIS J 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3069 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= 0.180 Angle : 0.534 10.534 29770 Z= 0.279 Chirality : 0.041 0.157 3354 Planarity : 0.003 0.050 3771 Dihedral : 5.080 27.050 2857 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.83 % Favored : 93.14 % Rotamer: Outliers : 2.60 % Allowed : 17.66 % Favored : 79.74 % 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: -3.15 (0.15), residues: 2637 helix: -1.47 (0.12), residues: 1562 sheet: -1.40 (0.35), residues: 179 loop : -3.18 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 280 HIS 0.012 0.001 HIS H 365 PHE 0.016 0.001 PHE I 195 TYR 0.019 0.001 TYR F 325 ARG 0.004 0.000 ARG G 473 *********************** 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 261 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 197 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: F 325 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.5885 (p90) REVERT: F 599 GLU cc_start: 0.4838 (OUTLIER) cc_final: 0.3711 (pp20) REVERT: G 109 MET cc_start: 0.8456 (mmt) cc_final: 0.8225 (mmm) REVERT: G 177 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: G 325 PHE cc_start: 0.8563 (t80) cc_final: 0.8218 (t80) REVERT: G 398 ASP cc_start: 0.7933 (m-30) cc_final: 0.7592 (m-30) REVERT: G 617 MET cc_start: 0.8314 (tpt) cc_final: 0.8098 (tpp) REVERT: G 862 MET cc_start: 0.8265 (mmp) cc_final: 0.7825 (mmm) REVERT: G 1102 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5091 (mt-10) REVERT: H 97 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5221 (t80) REVERT: H 102 GLU cc_start: 0.5401 (OUTLIER) cc_final: 0.5081 (mt-10) REVERT: H 365 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7555 (p90) REVERT: I 46 LEU cc_start: 0.7866 (pt) cc_final: 0.7564 (mm) REVERT: I 53 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6532 (tp) REVERT: J 119 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8490 (t0) REVERT: J 133 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6879 (mt-10) REVERT: J 151 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: J 229 MET cc_start: 0.1812 (mmt) cc_final: 0.0319 (ttm) REVERT: J 232 MET cc_start: 0.0820 (mmm) cc_final: -0.0693 (ttt) REVERT: J 234 GLN cc_start: 0.4077 (OUTLIER) cc_final: 0.3648 (pm20) outliers start: 64 outliers final: 35 residues processed: 242 average time/residue: 0.3039 time to fit residues: 119.4502 Evaluate side-chains 228 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 2.695 ------------------------------------------------------------------------------- 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 265 HIS Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 213 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 516 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 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 1102 GLU Chi-restraints excluded: chain G residue 1150 HIS Chi-restraints excluded: chain G residue 1162 ILE Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 102 GLU 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 313 CYS Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 365 HIS 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 119 ASN Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 151 GLU 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 85 optimal weight: 0.7980 chunk 228 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 211 optimal weight: 0.0010 chunk 117 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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** ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 365 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3238 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= 0.194 Angle : 0.540 10.183 29770 Z= 0.280 Chirality : 0.041 0.153 3354 Planarity : 0.003 0.049 3771 Dihedral : 4.944 26.781 2857 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.71 % Favored : 93.25 % Rotamer: Outliers : 2.68 % Allowed : 18.60 % Favored : 78.73 % 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: -2.79 (0.15), residues: 2637 helix: -1.18 (0.13), residues: 1565 sheet: -1.33 (0.35), residues: 179 loop : -3.04 (0.18), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 280 HIS 0.006 0.001 HIS H 53 PHE 0.018 0.001 PHE G1147 TYR 0.016 0.001 TYR F 325 ARG 0.003 0.000 ARG G 473 *********************** 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 244 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 178 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: F 325 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.5783 (p90) REVERT: F 495 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: F 599 GLU cc_start: 0.4898 (OUTLIER) cc_final: 0.3782 (pp20) REVERT: G 1 MET cc_start: 0.6573 (ppp) cc_final: 0.4521 (tmm) REVERT: G 109 MET cc_start: 0.8455 (mmt) cc_final: 0.8219 (mmm) REVERT: G 177 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7819 (mm-30) REVERT: G 325 PHE cc_start: 0.8536 (t80) cc_final: 0.8209 (t80) REVERT: G 398 ASP cc_start: 0.7990 (m-30) cc_final: 0.7642 (m-30) REVERT: G 617 MET cc_start: 0.8375 (tpt) cc_final: 0.8160 (tpp) REVERT: G 862 MET cc_start: 0.8243 (mmp) cc_final: 0.7801 (mmm) REVERT: H 97 PHE cc_start: 0.6097 (OUTLIER) cc_final: 0.5144 (t80) REVERT: H 102 GLU cc_start: 0.5248 (OUTLIER) cc_final: 0.5003 (mt-10) REVERT: H 365 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7493 (p90) REVERT: H 389 ARG cc_start: 0.6367 (tpt170) cc_final: 0.5973 (ttm-80) REVERT: I 46 LEU cc_start: 0.7833 (pt) cc_final: 0.7453 (mm) REVERT: I 53 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6477 (tp) REVERT: I 219 GLU cc_start: 0.7913 (tt0) cc_final: 0.7594 (tt0) REVERT: J 11 GLU cc_start: 0.6449 (tm-30) cc_final: 0.6188 (tm-30) REVERT: J 133 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6916 (mt-10) REVERT: J 151 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: J 229 MET cc_start: 0.1723 (mmt) cc_final: 0.0266 (ttm) REVERT: J 232 MET cc_start: 0.0898 (mmm) cc_final: -0.0643 (ttt) REVERT: J 234 GLN cc_start: 0.4163 (OUTLIER) cc_final: 0.3731 (pm20) outliers start: 66 outliers final: 39 residues processed: 228 average time/residue: 0.3082 time to fit residues: 113.0863 Evaluate side-chains 223 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 2.293 ------------------------------------------------------------------------------- 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 265 HIS Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 340 LYS 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 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 213 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 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 975 THR Chi-restraints excluded: chain G residue 1036 VAL 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 97 PHE Chi-restraints excluded: chain H residue 102 GLU 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 313 CYS Chi-restraints excluded: chain H residue 365 HIS 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 151 GLU 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 245 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 144 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 253 optimal weight: 0.4980 chunk 158 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 365 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3347 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= 0.194 Angle : 0.537 10.428 29770 Z= 0.278 Chirality : 0.041 0.208 3354 Planarity : 0.003 0.048 3771 Dihedral : 4.872 26.872 2857 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.48 % Favored : 93.48 % Rotamer: Outliers : 3.21 % Allowed : 18.51 % Favored : 78.28 % 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: -2.50 (0.15), residues: 2637 helix: -0.96 (0.13), residues: 1560 sheet: -1.28 (0.35), residues: 178 loop : -2.86 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 280 HIS 0.007 0.001 HIS H 365 PHE 0.015 0.001 PHE G 518 TYR 0.016 0.001 TYR G 432 ARG 0.002 0.000 ARG G 473 *********************** 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 257 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 178 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: F 325 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.5456 (p90) REVERT: F 495 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: F 581 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6172 (pp30) REVERT: F 599 GLU cc_start: 0.4897 (OUTLIER) cc_final: 0.3836 (pp20) REVERT: G 1 MET cc_start: 0.6566 (ppp) cc_final: 0.4498 (tmm) REVERT: G 17 VAL cc_start: 0.5367 (OUTLIER) cc_final: 0.5059 (t) REVERT: G 109 MET cc_start: 0.8448 (mmt) cc_final: 0.8196 (mmm) REVERT: G 177 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7819 (mm-30) REVERT: G 325 PHE cc_start: 0.8514 (t80) cc_final: 0.8184 (t80) REVERT: G 398 ASP cc_start: 0.8011 (m-30) cc_final: 0.7663 (m-30) REVERT: G 487 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.7910 (p-80) REVERT: G 617 MET cc_start: 0.8373 (tpt) cc_final: 0.8171 (tpp) REVERT: G 862 MET cc_start: 0.8238 (mmp) cc_final: 0.7792 (mmm) REVERT: G 957 HIS cc_start: 0.6968 (t70) cc_final: 0.6724 (t-90) REVERT: G 1028 LYS cc_start: 0.8635 (tppt) cc_final: 0.8287 (mmtp) REVERT: G 1062 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6579 (tt) REVERT: H 51 ARG cc_start: 0.6199 (mtp85) cc_final: 0.5979 (mtp85) REVERT: H 97 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5278 (t80) REVERT: H 102 GLU cc_start: 0.5300 (OUTLIER) cc_final: 0.5037 (mt-10) REVERT: H 104 TYR cc_start: 0.6686 (OUTLIER) cc_final: 0.5943 (p90) REVERT: H 365 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7511 (p90) REVERT: H 389 ARG cc_start: 0.6350 (tpt170) cc_final: 0.5983 (ttm-80) REVERT: I 46 LEU cc_start: 0.7795 (pt) cc_final: 0.7424 (mm) REVERT: I 219 GLU cc_start: 0.7888 (tt0) cc_final: 0.7577 (tt0) REVERT: J 11 GLU cc_start: 0.6541 (tm-30) cc_final: 0.6326 (tp30) REVERT: J 119 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8429 (t0) REVERT: J 133 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7023 (mt-10) REVERT: J 151 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: J 229 MET cc_start: 0.1937 (mmt) cc_final: 0.0450 (ttm) REVERT: J 232 MET cc_start: 0.0822 (mmm) cc_final: -0.0756 (ttt) REVERT: J 234 GLN cc_start: 0.3996 (OUTLIER) cc_final: 0.3661 (pm20) outliers start: 79 outliers final: 47 residues processed: 240 average time/residue: 0.3115 time to fit residues: 120.0332 Evaluate side-chains 234 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 171 time to evaluate : 2.475 ------------------------------------------------------------------------------- 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 188 LEU 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 325 TYR Chi-restraints excluded: chain F residue 340 LYS 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 581 GLN 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 213 MET Chi-restraints excluded: chain G residue 255 SER 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 487 HIS Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 516 THR 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 1150 HIS Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 117 ASP 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 273 ILE 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 H residue 365 HIS 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 119 ASN Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 151 GLU 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 156 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 172 optimal weight: 0.0870 chunk 125 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 199 optimal weight: 0.5980 chunk 230 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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** ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 365 HIS J 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22042 Z= 0.183 Angle : 0.535 10.683 29770 Z= 0.275 Chirality : 0.041 0.233 3354 Planarity : 0.003 0.060 3771 Dihedral : 4.779 26.519 2857 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.37 % Favored : 93.59 % Rotamer: Outliers : 3.00 % Allowed : 18.80 % Favored : 78.20 % 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: -2.26 (0.16), residues: 2637 helix: -0.74 (0.13), residues: 1549 sheet: -1.22 (0.37), residues: 167 loop : -2.78 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 280 HIS 0.010 0.001 HIS H 365 PHE 0.014 0.001 PHE G 518 TYR 0.015 0.001 TYR G 432 ARG 0.002 0.000 ARG J 59 *********************** 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 260 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 186 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: F 325 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.5451 (p90) REVERT: F 495 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: F 581 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6164 (pp30) REVERT: F 599 GLU cc_start: 0.4874 (OUTLIER) cc_final: 0.3809 (pp20) REVERT: G 17 VAL cc_start: 0.5340 (OUTLIER) cc_final: 0.5079 (t) REVERT: G 109 MET cc_start: 0.8451 (mmt) cc_final: 0.8207 (mmm) REVERT: G 177 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: G 325 PHE cc_start: 0.8501 (t80) cc_final: 0.8179 (t80) REVERT: G 398 ASP cc_start: 0.8025 (m-30) cc_final: 0.7677 (m-30) REVERT: G 487 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7884 (p-80) REVERT: G 862 MET cc_start: 0.8236 (mmp) cc_final: 0.7787 (mmm) REVERT: G 1062 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6587 (tt) REVERT: H 51 ARG cc_start: 0.6145 (mtp85) cc_final: 0.5938 (mtp85) REVERT: H 97 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.5425 (t80) REVERT: H 102 GLU cc_start: 0.5328 (OUTLIER) cc_final: 0.5060 (mt-10) REVERT: H 104 TYR cc_start: 0.6691 (OUTLIER) cc_final: 0.5875 (p90) REVERT: H 365 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.7489 (p90) REVERT: H 389 ARG cc_start: 0.6376 (tpt170) cc_final: 0.6021 (ttm-80) REVERT: I 103 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6285 (mp) REVERT: J 119 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8452 (t0) REVERT: J 133 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6984 (mt-10) REVERT: J 151 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: J 229 MET cc_start: 0.1690 (mmt) cc_final: 0.0271 (ttm) REVERT: J 232 MET cc_start: 0.0804 (mmm) cc_final: -0.0771 (ttt) REVERT: J 234 GLN cc_start: 0.3568 (OUTLIER) cc_final: 0.3308 (pm20) outliers start: 74 outliers final: 48 residues processed: 243 average time/residue: 0.3053 time to fit residues: 120.6879 Evaluate side-chains 246 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 181 time to evaluate : 2.685 ------------------------------------------------------------------------------- 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 188 LEU 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 325 TYR Chi-restraints excluded: chain F residue 340 LYS 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 581 GLN 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 213 MET Chi-restraints excluded: chain G residue 255 SER 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 487 HIS 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 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 G residue 1150 HIS Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 117 ASP 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 273 ILE 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 H residue 365 HIS Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 103 LEU 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 119 ASN Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 151 GLU 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 242 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 72 optimal weight: 0.0050 chunk 213 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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** ** G1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 365 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22042 Z= 0.210 Angle : 0.557 10.359 29770 Z= 0.284 Chirality : 0.042 0.224 3354 Planarity : 0.003 0.048 3771 Dihedral : 4.798 27.202 2857 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.33 % Favored : 93.63 % Rotamer: Outliers : 2.92 % Allowed : 18.84 % Favored : 78.24 % 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: -2.19 (0.16), residues: 2637 helix: -0.65 (0.13), residues: 1550 sheet: -1.24 (0.37), residues: 167 loop : -2.80 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 280 HIS 0.011 0.001 HIS H 365 PHE 0.014 0.001 PHE G 518 TYR 0.018 0.001 TYR G 432 ARG 0.004 0.000 ARG G 473 *********************** 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 254 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 182 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: F 325 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.5470 (p90) REVERT: F 495 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: F 581 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6177 (pp30) REVERT: F 599 GLU cc_start: 0.4890 (OUTLIER) cc_final: 0.3831 (pp20) REVERT: G 1 MET cc_start: 0.6218 (ppp) cc_final: 0.4443 (ttp) REVERT: G 17 VAL cc_start: 0.5233 (OUTLIER) cc_final: 0.5019 (t) REVERT: G 109 MET cc_start: 0.8471 (mmt) cc_final: 0.8195 (mmm) REVERT: G 177 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: G 398 ASP cc_start: 0.8044 (m-30) cc_final: 0.7680 (m-30) REVERT: G 487 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.8000 (p-80) REVERT: G 1062 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6539 (tt) REVERT: G 1070 ILE cc_start: 0.6794 (mm) cc_final: 0.6558 (mt) REVERT: H 51 ARG cc_start: 0.6117 (mtp85) cc_final: 0.5917 (mtp85) REVERT: H 97 PHE cc_start: 0.6481 (OUTLIER) cc_final: 0.5543 (t80) REVERT: H 99 LYS cc_start: 0.5683 (ttmm) cc_final: 0.4741 (ttmm) REVERT: H 102 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.5144 (mt-10) REVERT: H 104 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.5898 (p90) REVERT: H 365 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7484 (p90) REVERT: H 389 ARG cc_start: 0.6351 (tpt170) cc_final: 0.6018 (ttm-80) REVERT: I 103 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6388 (mp) REVERT: J 119 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8565 (t0) REVERT: J 133 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7081 (mt-10) REVERT: J 151 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: J 229 MET cc_start: 0.1703 (mmt) cc_final: 0.0283 (ttm) REVERT: J 232 MET cc_start: 0.0827 (mmm) cc_final: -0.0764 (ttt) REVERT: J 234 GLN cc_start: 0.3577 (OUTLIER) cc_final: 0.3321 (pm20) outliers start: 72 outliers final: 48 residues processed: 235 average time/residue: 0.3063 time to fit residues: 116.5510 Evaluate side-chains 239 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 174 time to evaluate : 2.536 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 265 HIS 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 581 GLN 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 213 MET Chi-restraints excluded: chain G residue 255 SER 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 487 HIS 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 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 1077 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 97 PHE Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 117 ASP 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 273 ILE 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 H residue 365 HIS Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 103 LEU 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 119 ASN Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 234 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 249 optimal weight: 2.9990 chunk 152 optimal weight: 0.0970 chunk 118 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 262 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 chunk 208 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 161 optimal weight: 0.3980 chunk 127 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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** H 365 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22042 Z= 0.145 Angle : 0.529 11.127 29770 Z= 0.269 Chirality : 0.040 0.236 3354 Planarity : 0.003 0.046 3771 Dihedral : 4.576 25.485 2857 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.07 % Favored : 93.89 % Rotamer: Outliers : 2.35 % Allowed : 19.69 % Favored : 77.95 % 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: -1.95 (0.16), residues: 2637 helix: -0.42 (0.13), residues: 1552 sheet: -1.22 (0.37), residues: 167 loop : -2.77 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 90 HIS 0.010 0.001 HIS H 365 PHE 0.013 0.001 PHE H 97 TYR 0.014 0.001 TYR G 808 ARG 0.004 0.000 ARG G 473 ********************** 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 244 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 186 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: F 325 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.5421 (p90) REVERT: F 599 GLU cc_start: 0.4802 (OUTLIER) cc_final: 0.3804 (pp20) REVERT: G 1 MET cc_start: 0.6186 (ppp) cc_final: 0.4507 (ttp) REVERT: G 109 MET cc_start: 0.8413 (mmt) cc_final: 0.8177 (mmm) REVERT: G 177 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7782 (mm-30) REVERT: G 487 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7764 (p-80) REVERT: G 1070 ILE cc_start: 0.6666 (mm) cc_final: 0.6447 (mt) REVERT: H 97 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.5673 (t80) REVERT: H 102 GLU cc_start: 0.5383 (OUTLIER) cc_final: 0.4845 (mt-10) REVERT: H 104 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.5815 (p90) REVERT: H 365 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7403 (p90) REVERT: H 389 ARG cc_start: 0.6285 (tpt170) cc_final: 0.5984 (ttm-80) REVERT: J 119 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8464 (t0) REVERT: J 133 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6969 (mt-10) REVERT: J 141 VAL cc_start: 0.6798 (OUTLIER) cc_final: 0.6551 (p) REVERT: J 151 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: J 229 MET cc_start: 0.1615 (mmt) cc_final: 0.0184 (ttm) REVERT: J 232 MET cc_start: 0.0582 (mmm) cc_final: -0.0988 (ttt) REVERT: J 234 GLN cc_start: 0.3547 (OUTLIER) cc_final: 0.3258 (pm20) outliers start: 58 outliers final: 35 residues processed: 228 average time/residue: 0.3100 time to fit residues: 115.8292 Evaluate side-chains 221 residues out of total 2465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 173 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 265 HIS 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 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 213 MET Chi-restraints excluded: chain G residue 255 SER 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 487 HIS 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 1027 ILE 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 97 PHE Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 104 TYR 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 335 LEU Chi-restraints excluded: chain H residue 365 HIS 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 119 ASN Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 234 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** H 365 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.153450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111547 restraints weight = 33091.224| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.65 r_work: 0.3240 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22042 Z= 0.176 Angle : 0.550 11.024 29770 Z= 0.277 Chirality : 0.041 0.224 3354 Planarity : 0.003 0.045 3771 Dihedral : 4.589 24.463 2857 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.18 % Favored : 93.78 % Rotamer: Outliers : 2.23 % Allowed : 19.81 % Favored : 77.95 % 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: -0.34 (0.13), residues: 1553 sheet: -1.18 (0.38), residues: 168 loop : -2.73 (0.18), residues: 916 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 0.017 0.001 PHE I 195 TYR 0.015 0.001 TYR G 432 ARG 0.003 0.000 ARG G 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.90 seconds wall clock time: 87 minutes 18.24 seconds (5238.24 seconds total)