Starting phenix.real_space_refine on Fri Mar 15 08:07:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1x_41837/03_2024/8u1x_41837.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1x_41837/03_2024/8u1x_41837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1x_41837/03_2024/8u1x_41837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1x_41837/03_2024/8u1x_41837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1x_41837/03_2024/8u1x_41837.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1x_41837/03_2024/8u1x_41837.pdb" } resolution = 2.7 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= 0.030 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: 5 Type Number sf(0) Gaussians Mn 2 7.51 5 S 58 5.16 5 C 7057 2.51 5 N 1872 2.21 5 O 2051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11040 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4513 Classifications: {'peptide': 579} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 552} Chain: "B" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 4049 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 29, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2476 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 294} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.62, per 1000 atoms: 0.51 Number of scatterers: 11040 At special positions: 0 Unit cell: (104.664, 116.412, 118.548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 2 24.99 S 58 16.00 O 2051 8.00 N 1872 7.00 C 7057 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.8 seconds 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 3 sheets defined 68.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 4.103A pdb=" N LEU A 16 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 19 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 34 removed outlier: 3.544A pdb=" N ARG A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.555A pdb=" N SER A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.534A pdb=" N LYS A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 removed outlier: 4.259A pdb=" N GLU A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 140 through 147 removed outlier: 3.642A pdb=" N ARG A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 151 removed outlier: 3.986A pdb=" N PHE A 151 " --> pdb=" O CYS A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.519A pdb=" N GLU A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.693A pdb=" N MET A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.078A pdb=" N LEU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 235 No H-bonds generated for 'chain 'A' and resid 234 through 235' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.658A pdb=" N GLU A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.519A pdb=" N THR A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.906A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.917A pdb=" N CYS A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.968A pdb=" N GLU A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.696A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 351 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.558A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 Processing helix chain 'A' and resid 365 through 374 removed outlier: 3.586A pdb=" N LYS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.506A pdb=" N SER A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.892A pdb=" N VAL A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 404 removed outlier: 3.592A pdb=" N GLN A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.531A pdb=" N ILE A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Proline residue: A 428 - end of helix removed outlier: 3.710A pdb=" N GLN A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.840A pdb=" N GLU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 removed outlier: 3.621A pdb=" N CYS A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 474 removed outlier: 3.518A pdb=" N SER A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.533A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.658A pdb=" N ALA A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 494 through 520 removed outlier: 3.744A pdb=" N THR A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 507 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLN A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N ASP A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 533 through 547 removed outlier: 3.530A pdb=" N ARG A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.520A pdb=" N LYS A 566 " --> pdb=" O PRO A 562 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.713A pdb=" N THR A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 Processing helix chain 'B' and resid 138 through 159 removed outlier: 3.636A pdb=" N VAL B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.645A pdb=" N ASN B 178 " --> pdb=" O MET B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.916A pdb=" N ASP B 199 " --> pdb=" O PRO B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 222 removed outlier: 4.961A pdb=" N LEU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 251 through 269 removed outlier: 3.503A pdb=" N PHE B 257 " --> pdb=" O ARG B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 290 Processing helix chain 'B' and resid 296 through 309 removed outlier: 3.757A pdb=" N SER B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 326 Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.553A pdb=" N LYS B 332 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 333 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 removed outlier: 4.178A pdb=" N TYR B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.553A pdb=" N TYR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.653A pdb=" N GLU B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 3.672A pdb=" N SER B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 removed outlier: 3.688A pdb=" N GLN B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 423 Processing helix chain 'B' and resid 424 through 427 Processing helix chain 'B' and resid 428 through 437 Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.653A pdb=" N LEU B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Proline residue: B 444 - end of helix Proline residue: B 448 - end of helix Processing helix chain 'B' and resid 460 through 475 removed outlier: 3.560A pdb=" N GLY B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 505 removed outlier: 3.694A pdb=" N LYS B 500 " --> pdb=" O ARG B 496 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 501 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 509 removed outlier: 3.851A pdb=" N ILE B 509 " --> pdb=" O TRP B 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 506 through 509' Processing helix chain 'B' and resid 578 through 588 removed outlier: 3.556A pdb=" N HIS B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 removed outlier: 3.512A pdb=" N THR C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 9 " --> pdb=" O VAL C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.520A pdb=" N GLU C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 38 " --> pdb=" O LYS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.520A pdb=" N ARG C 70 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 140 through 150 removed outlier: 3.596A pdb=" N LYS C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' Processing helix chain 'C' and resid 176 through 182 removed outlier: 3.641A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.602A pdb=" N SER C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.194A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.372A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.602A pdb=" N ASP C 202 " --> pdb=" O PHE C 220 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2074 1.32 - 1.44: 2666 1.44 - 1.57: 6446 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 11273 Sorted by residual: bond pdb=" C LEU A 52 " pdb=" N PRO A 53 " ideal model delta sigma weight residual 1.336 1.374 -0.038 1.23e-02 6.61e+03 9.64e+00 bond pdb=" CA GLY C 215 " pdb=" C GLY C 215 " ideal model delta sigma weight residual 1.515 1.475 0.040 1.32e-02 5.74e+03 9.28e+00 bond pdb=" N LEU B 183 " pdb=" CA LEU B 183 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.14e-02 7.69e+03 8.41e+00 bond pdb=" N HIS C 299 " pdb=" CA HIS C 299 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.14e+00 bond pdb=" C LEU A 90 " pdb=" N PRO A 91 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.61e+00 ... (remaining 11268 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.31: 254 105.31 - 112.49: 5625 112.49 - 119.67: 4140 119.67 - 126.84: 5107 126.84 - 134.02: 146 Bond angle restraints: 15272 Sorted by residual: angle pdb=" N ILE B 167 " pdb=" CA ILE B 167 " pdb=" C ILE B 167 " ideal model delta sigma weight residual 112.96 107.77 5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 113.01 107.17 5.84 1.20e+00 6.94e-01 2.37e+01 angle pdb=" CA PRO A 91 " pdb=" C PRO A 91 " pdb=" N PRO A 92 " ideal model delta sigma weight residual 117.93 123.69 -5.76 1.20e+00 6.94e-01 2.31e+01 angle pdb=" C ALA C 216 " pdb=" N GLY C 217 " pdb=" CA GLY C 217 " ideal model delta sigma weight residual 122.66 115.52 7.14 1.77e+00 3.19e-01 1.62e+01 angle pdb=" CA ARG A 21 " pdb=" CB ARG A 21 " pdb=" CG ARG A 21 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 ... (remaining 15267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 6128 15.86 - 31.71: 579 31.71 - 47.57: 153 47.57 - 63.43: 21 63.43 - 79.28: 9 Dihedral angle restraints: 6890 sinusoidal: 2833 harmonic: 4057 Sorted by residual: dihedral pdb=" CA GLU B 491 " pdb=" C GLU B 491 " pdb=" N LYS B 492 " pdb=" CA LYS B 492 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ARG B 123 " pdb=" C ARG B 123 " pdb=" N GLN B 124 " pdb=" CA GLN B 124 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ARG C 268 " pdb=" C ARG C 268 " pdb=" N CYS C 269 " pdb=" CA CYS C 269 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1190 0.048 - 0.095: 416 0.095 - 0.143: 92 0.143 - 0.191: 24 0.191 - 0.239: 2 Chirality restraints: 1724 Sorted by residual: chirality pdb=" CB VAL B 399 " pdb=" CA VAL B 399 " pdb=" CG1 VAL B 399 " pdb=" CG2 VAL B 399 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ARG B 181 " pdb=" N ARG B 181 " pdb=" C ARG B 181 " pdb=" CB ARG B 181 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CA ILE B 72 " pdb=" N ILE B 72 " pdb=" C ILE B 72 " pdb=" CB ILE B 72 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 1721 not shown) Planarity restraints: 1966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 178 " 0.022 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C ASN B 178 " -0.078 2.00e-02 2.50e+03 pdb=" O ASN B 178 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU B 179 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP B 207 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO B 208 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 215 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C GLY C 215 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY C 215 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA C 216 " 0.017 2.00e-02 2.50e+03 ... (remaining 1963 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 69 2.57 - 3.15: 8149 3.15 - 3.74: 16997 3.74 - 4.32: 25384 4.32 - 4.90: 40374 Nonbonded interactions: 90973 Sorted by model distance: nonbonded pdb=" ND1 HIS C 241 " pdb="MN MN C 401 " model vdw 1.988 2.400 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 402 " model vdw 2.081 2.320 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 401 " model vdw 2.084 2.320 nonbonded pdb=" CE1 HIS C 59 " pdb="MN MN C 402 " model vdw 2.102 2.540 nonbonded pdb=" OD1 ASN C 117 " pdb="MN MN C 401 " model vdw 2.116 2.320 ... (remaining 90968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.090 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 0.061 11273 Z= 0.382 Angle : 0.817 9.189 15272 Z= 0.468 Chirality : 0.051 0.239 1724 Planarity : 0.008 0.120 1966 Dihedral : 13.608 79.285 4248 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.72 (0.14), residues: 1367 helix: -4.50 (0.07), residues: 829 sheet: -1.90 (0.71), residues: 48 loop : -2.19 (0.22), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 207 HIS 0.004 0.001 HIS B 340 PHE 0.029 0.002 PHE A 538 TYR 0.013 0.001 TYR A 60 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.194 Fit side-chains REVERT: A 16 LEU cc_start: 0.8058 (mm) cc_final: 0.7248 (pp) REVERT: A 30 ASN cc_start: 0.8426 (m110) cc_final: 0.8092 (m110) REVERT: A 50 GLU cc_start: 0.8016 (mp0) cc_final: 0.7603 (mp0) REVERT: A 140 TRP cc_start: 0.8178 (m100) cc_final: 0.7833 (m100) REVERT: A 177 ASP cc_start: 0.8593 (m-30) cc_final: 0.8360 (m-30) REVERT: B 165 GLU cc_start: 0.8616 (pt0) cc_final: 0.8299 (pm20) REVERT: B 199 ASP cc_start: 0.8485 (m-30) cc_final: 0.8283 (m-30) REVERT: B 572 LYS cc_start: 0.8389 (ptmm) cc_final: 0.8055 (ptmt) REVERT: B 578 ASP cc_start: 0.7410 (t0) cc_final: 0.6938 (t0) REVERT: C 245 MET cc_start: 0.8873 (mmt) cc_final: 0.8667 (mmt) outliers start: 0 outliers final: 1 residues processed: 140 average time/residue: 1.4399 time to fit residues: 215.3013 Evaluate side-chains 89 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 312 ASN A 465 ASN A 545 GLN B 87 GLN B 93 ASN B 124 GLN B 463 HIS B 478 GLN B 493 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11273 Z= 0.208 Angle : 0.583 7.639 15272 Z= 0.306 Chirality : 0.041 0.146 1724 Planarity : 0.005 0.047 1966 Dihedral : 4.845 23.031 1492 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.14 % Allowed : 9.97 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.07 (0.19), residues: 1367 helix: -2.06 (0.15), residues: 843 sheet: -1.71 (0.68), residues: 53 loop : -1.65 (0.24), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 506 HIS 0.002 0.001 HIS B 340 PHE 0.031 0.001 PHE A 538 TYR 0.015 0.001 TYR A 169 ARG 0.011 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7878 (mm) cc_final: 0.7143 (pp) REVERT: A 30 ASN cc_start: 0.8247 (m110) cc_final: 0.7806 (m110) REVERT: A 46 ARG cc_start: 0.8407 (ptm160) cc_final: 0.8054 (ptm160) REVERT: A 50 GLU cc_start: 0.8025 (mp0) cc_final: 0.7645 (mp0) REVERT: A 140 TRP cc_start: 0.8178 (m100) cc_final: 0.7848 (m100) REVERT: A 442 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9045 (mmmm) REVERT: B 116 GLU cc_start: 0.8332 (tp30) cc_final: 0.8095 (tp30) REVERT: B 198 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8442 (mt-10) REVERT: B 199 ASP cc_start: 0.8492 (m-30) cc_final: 0.8266 (m-30) REVERT: B 578 ASP cc_start: 0.6928 (t0) cc_final: 0.6430 (t0) REVERT: B 592 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7841 (mt-10) outliers start: 14 outliers final: 6 residues processed: 105 average time/residue: 1.5465 time to fit residues: 173.6038 Evaluate side-chains 92 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 304 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 102 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.0304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11273 Z= 0.214 Angle : 0.558 6.344 15272 Z= 0.286 Chirality : 0.041 0.137 1724 Planarity : 0.004 0.049 1966 Dihedral : 4.494 21.120 1492 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.88 % Allowed : 10.70 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.21), residues: 1367 helix: -0.67 (0.17), residues: 846 sheet: -0.93 (0.80), residues: 43 loop : -1.36 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 506 HIS 0.003 0.000 HIS B 340 PHE 0.030 0.001 PHE A 538 TYR 0.010 0.001 TYR C 86 ARG 0.007 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8033 (mp0) cc_final: 0.7622 (mp0) REVERT: A 140 TRP cc_start: 0.8214 (m100) cc_final: 0.7822 (m100) REVERT: A 231 ILE cc_start: 0.9239 (mt) cc_final: 0.9025 (mp) REVERT: B 116 GLU cc_start: 0.8559 (tp30) cc_final: 0.8342 (tp30) REVERT: B 198 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8476 (mt-10) REVERT: B 578 ASP cc_start: 0.6765 (t0) cc_final: 0.6264 (t0) REVERT: B 592 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7882 (mt-10) outliers start: 23 outliers final: 11 residues processed: 101 average time/residue: 1.4248 time to fit residues: 154.5019 Evaluate side-chains 91 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 304 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 0.0970 chunk 130 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11273 Z= 0.260 Angle : 0.561 8.067 15272 Z= 0.285 Chirality : 0.042 0.150 1724 Planarity : 0.004 0.045 1966 Dihedral : 4.407 22.806 1492 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.72 % Allowed : 11.76 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.23), residues: 1367 helix: 0.02 (0.18), residues: 856 sheet: -0.53 (0.93), residues: 36 loop : -1.27 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 506 HIS 0.003 0.001 HIS B 340 PHE 0.028 0.001 PHE A 538 TYR 0.016 0.001 TYR A 169 ARG 0.013 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8057 (mp0) cc_final: 0.7613 (mp0) REVERT: A 71 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8398 (tp30) REVERT: A 140 TRP cc_start: 0.8284 (m100) cc_final: 0.7917 (m100) REVERT: A 231 ILE cc_start: 0.9241 (mt) cc_final: 0.9014 (mp) REVERT: B 116 GLU cc_start: 0.8725 (tp30) cc_final: 0.8467 (tp30) REVERT: B 198 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8483 (mt-10) REVERT: B 578 ASP cc_start: 0.6731 (t0) cc_final: 0.6319 (t0) REVERT: B 592 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7820 (mt-10) outliers start: 21 outliers final: 12 residues processed: 93 average time/residue: 1.3895 time to fit residues: 139.2400 Evaluate side-chains 90 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 304 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.0170 chunk 111 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 32 optimal weight: 0.0040 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11273 Z= 0.135 Angle : 0.508 8.952 15272 Z= 0.257 Chirality : 0.039 0.138 1724 Planarity : 0.004 0.044 1966 Dihedral : 4.116 19.334 1492 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.72 % Allowed : 12.01 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1367 helix: 0.59 (0.19), residues: 845 sheet: -0.51 (0.83), residues: 43 loop : -0.93 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 506 HIS 0.001 0.000 HIS B 340 PHE 0.026 0.001 PHE A 538 TYR 0.011 0.001 TYR C 86 ARG 0.008 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.233 Fit side-chains REVERT: A 50 GLU cc_start: 0.8005 (mp0) cc_final: 0.7553 (mp0) REVERT: A 62 GLU cc_start: 0.7335 (mp0) cc_final: 0.7064 (mm-30) REVERT: A 71 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8396 (tp30) REVERT: A 140 TRP cc_start: 0.8218 (m100) cc_final: 0.7804 (m100) REVERT: A 231 ILE cc_start: 0.9218 (mt) cc_final: 0.8963 (mp) REVERT: B 116 GLU cc_start: 0.8826 (tp30) cc_final: 0.8535 (tp30) REVERT: B 198 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8476 (mt-10) REVERT: B 506 TRP cc_start: 0.4954 (t60) cc_final: 0.4386 (m100) REVERT: B 574 GLU cc_start: 0.7444 (tp30) cc_final: 0.7235 (tp30) REVERT: B 578 ASP cc_start: 0.6712 (t0) cc_final: 0.6289 (t0) REVERT: B 592 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7862 (mt-10) outliers start: 21 outliers final: 13 residues processed: 105 average time/residue: 1.2488 time to fit residues: 141.6599 Evaluate side-chains 97 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 306 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11273 Z= 0.219 Angle : 0.543 10.070 15272 Z= 0.272 Chirality : 0.041 0.137 1724 Planarity : 0.004 0.053 1966 Dihedral : 4.115 20.738 1492 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.88 % Allowed : 12.50 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1367 helix: 0.80 (0.19), residues: 847 sheet: -0.90 (0.82), residues: 46 loop : -0.84 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 506 HIS 0.002 0.000 HIS B 340 PHE 0.026 0.001 PHE A 538 TYR 0.011 0.001 TYR C 86 ARG 0.017 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8022 (mp0) cc_final: 0.7570 (mp0) REVERT: A 62 GLU cc_start: 0.7459 (mp0) cc_final: 0.7112 (mm-30) REVERT: A 71 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8464 (tp30) REVERT: A 140 TRP cc_start: 0.8256 (m100) cc_final: 0.7872 (m100) REVERT: B 100 LEU cc_start: 0.8782 (mt) cc_final: 0.8520 (mt) REVERT: B 116 GLU cc_start: 0.8926 (tp30) cc_final: 0.8662 (tp30) REVERT: B 198 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8470 (mt-10) REVERT: B 578 ASP cc_start: 0.6698 (t0) cc_final: 0.6245 (t0) REVERT: B 592 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: C 4 LYS cc_start: 0.8099 (mppt) cc_final: 0.7682 (tptt) outliers start: 23 outliers final: 14 residues processed: 101 average time/residue: 1.4797 time to fit residues: 160.9344 Evaluate side-chains 100 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 306 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.0170 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11273 Z= 0.180 Angle : 0.529 11.129 15272 Z= 0.266 Chirality : 0.040 0.179 1724 Planarity : 0.004 0.040 1966 Dihedral : 4.036 22.552 1490 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.72 % Allowed : 12.99 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1367 helix: 0.98 (0.19), residues: 844 sheet: -0.37 (0.84), residues: 43 loop : -0.81 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 506 HIS 0.002 0.000 HIS B 340 PHE 0.025 0.001 PHE A 538 TYR 0.011 0.001 TYR C 86 ARG 0.006 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8016 (mp0) cc_final: 0.7564 (mp0) REVERT: A 62 GLU cc_start: 0.7400 (mp0) cc_final: 0.7089 (mm-30) REVERT: A 71 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8471 (tp30) REVERT: A 140 TRP cc_start: 0.8237 (m100) cc_final: 0.7809 (m100) REVERT: A 341 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8117 (t) REVERT: B 100 LEU cc_start: 0.8815 (mt) cc_final: 0.8600 (mt) REVERT: B 101 GLN cc_start: 0.8401 (pm20) cc_final: 0.8099 (pm20) REVERT: B 116 GLU cc_start: 0.8942 (tp30) cc_final: 0.8689 (tp30) REVERT: B 198 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8443 (mt-10) REVERT: B 441 ARG cc_start: 0.8687 (ptt-90) cc_final: 0.8447 (ptt-90) REVERT: B 443 LEU cc_start: 0.9228 (mt) cc_final: 0.8973 (tm) REVERT: B 578 ASP cc_start: 0.6762 (t0) cc_final: 0.6290 (t0) REVERT: B 592 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: C 4 LYS cc_start: 0.7944 (mppt) cc_final: 0.7431 (mmmm) outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 1.4447 time to fit residues: 158.3836 Evaluate side-chains 102 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 306 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 124 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11273 Z= 0.160 Angle : 0.533 11.850 15272 Z= 0.267 Chirality : 0.040 0.243 1724 Planarity : 0.004 0.076 1966 Dihedral : 3.977 22.246 1490 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.23 % Allowed : 13.56 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1367 helix: 1.11 (0.19), residues: 842 sheet: -0.20 (0.92), residues: 36 loop : -0.73 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 506 HIS 0.002 0.000 HIS B 340 PHE 0.024 0.001 PHE A 538 TYR 0.012 0.001 TYR C 86 ARG 0.014 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.371 Fit side-chains REVERT: A 50 GLU cc_start: 0.8015 (mp0) cc_final: 0.7575 (mp0) REVERT: A 62 GLU cc_start: 0.7385 (mp0) cc_final: 0.7062 (mm-30) REVERT: A 71 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8480 (tp30) REVERT: A 140 TRP cc_start: 0.8222 (m100) cc_final: 0.7813 (m100) REVERT: A 231 ILE cc_start: 0.9220 (mt) cc_final: 0.8953 (mp) REVERT: A 341 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8110 (t) REVERT: B 100 LEU cc_start: 0.8818 (mt) cc_final: 0.8605 (mt) REVERT: B 101 GLN cc_start: 0.8385 (pm20) cc_final: 0.8094 (pm20) REVERT: B 116 GLU cc_start: 0.8961 (tp30) cc_final: 0.8710 (tp30) REVERT: B 198 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8393 (mt-10) REVERT: B 443 LEU cc_start: 0.9208 (mt) cc_final: 0.8937 (tm) REVERT: B 578 ASP cc_start: 0.6702 (t0) cc_final: 0.6199 (t0) REVERT: B 592 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7809 (mt-10) outliers start: 15 outliers final: 8 residues processed: 102 average time/residue: 1.4185 time to fit residues: 155.6263 Evaluate side-chains 95 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 304 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11273 Z= 0.237 Angle : 0.565 13.025 15272 Z= 0.283 Chirality : 0.042 0.242 1724 Planarity : 0.004 0.045 1966 Dihedral : 4.027 21.489 1490 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.39 % Allowed : 13.89 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1367 helix: 1.13 (0.19), residues: 841 sheet: -0.86 (0.75), residues: 53 loop : -0.68 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 506 HIS 0.002 0.000 HIS A 520 PHE 0.033 0.001 PHE B 481 TYR 0.013 0.001 TYR C 86 ARG 0.007 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.334 Fit side-chains REVERT: A 16 LEU cc_start: 0.7737 (mm) cc_final: 0.7012 (pp) REVERT: A 50 GLU cc_start: 0.8035 (mp0) cc_final: 0.7588 (mp0) REVERT: A 62 GLU cc_start: 0.7376 (mp0) cc_final: 0.7158 (mm-30) REVERT: A 71 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8480 (tp30) REVERT: A 140 TRP cc_start: 0.8259 (m100) cc_final: 0.7840 (m100) REVERT: A 231 ILE cc_start: 0.9229 (mt) cc_final: 0.8987 (mp) REVERT: B 100 LEU cc_start: 0.8821 (mt) cc_final: 0.8608 (mt) REVERT: B 101 GLN cc_start: 0.8389 (pm20) cc_final: 0.8098 (pm20) REVERT: B 116 GLU cc_start: 0.8960 (tp30) cc_final: 0.8711 (tp30) REVERT: B 198 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8373 (mt-10) REVERT: B 443 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8923 (tm) REVERT: B 578 ASP cc_start: 0.6688 (t0) cc_final: 0.6211 (t0) REVERT: B 592 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7842 (mt-10) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 1.4142 time to fit residues: 148.1862 Evaluate side-chains 98 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 306 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 123 optimal weight: 0.0870 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11273 Z= 0.149 Angle : 0.550 13.553 15272 Z= 0.274 Chirality : 0.039 0.225 1724 Planarity : 0.004 0.076 1966 Dihedral : 3.941 21.742 1490 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.90 % Allowed : 14.38 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1367 helix: 1.25 (0.19), residues: 843 sheet: -0.05 (0.98), residues: 31 loop : -0.73 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 506 HIS 0.002 0.000 HIS A 520 PHE 0.026 0.001 PHE B 481 TYR 0.012 0.001 TYR C 86 ARG 0.019 0.000 ARG C 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.295 Fit side-chains REVERT: A 50 GLU cc_start: 0.7996 (mp0) cc_final: 0.7560 (mp0) REVERT: A 71 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8498 (tp30) REVERT: A 140 TRP cc_start: 0.8222 (m100) cc_final: 0.7813 (m100) REVERT: A 165 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8309 (mm-30) REVERT: A 231 ILE cc_start: 0.9216 (mt) cc_final: 0.8948 (mp) REVERT: B 100 LEU cc_start: 0.8815 (mt) cc_final: 0.8604 (mt) REVERT: B 101 GLN cc_start: 0.8387 (pm20) cc_final: 0.8092 (pm20) REVERT: B 198 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8351 (mt-10) REVERT: B 443 LEU cc_start: 0.9148 (mt) cc_final: 0.8896 (tm) REVERT: B 578 ASP cc_start: 0.6647 (t0) cc_final: 0.6165 (t0) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 1.4757 time to fit residues: 155.0882 Evaluate side-chains 94 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 19 optimal weight: 0.0270 chunk 94 optimal weight: 2.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.067264 restraints weight = 19344.729| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.76 r_work: 0.2665 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11273 Z= 0.220 Angle : 0.577 13.739 15272 Z= 0.285 Chirality : 0.041 0.233 1724 Planarity : 0.004 0.044 1966 Dihedral : 3.960 21.446 1490 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.06 % Allowed : 14.22 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1367 helix: 1.29 (0.19), residues: 841 sheet: -0.81 (0.75), residues: 53 loop : -0.65 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 506 HIS 0.002 0.000 HIS A 520 PHE 0.026 0.001 PHE B 481 TYR 0.011 0.001 TYR C 86 ARG 0.009 0.000 ARG B 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3424.55 seconds wall clock time: 61 minutes 23.26 seconds (3683.26 seconds total)