Starting phenix.real_space_refine on Sat Mar 16 17:15:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tek_41189/03_2024/8tek_41189.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tek_41189/03_2024/8tek_41189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tek_41189/03_2024/8tek_41189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tek_41189/03_2024/8tek_41189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tek_41189/03_2024/8tek_41189.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tek_41189/03_2024/8tek_41189.pdb" } resolution = 3.6 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= -0.001 sd= 0.005 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 40 5.16 5 C 9612 2.51 5 N 2714 2.21 5 O 2884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 445": "OD1" <-> "OD2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "E ASP 329": "OD1" <-> "OD2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "E GLU 374": "OE1" <-> "OE2" Residue "M TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 203": "OE1" <-> "OE2" Residue "M GLU 293": "OE1" <-> "OE2" Residue "N TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 614": "OE1" <-> "OE2" Residue "N GLU 639": "OE1" <-> "OE2" Residue "N GLU 652": "OE1" <-> "OE2" Residue "N GLU 672": "OE1" <-> "OE2" Residue "N GLU 689": "OE1" <-> "OE2" Residue "O GLU 616": "OE1" <-> "OE2" Residue "O GLU 629": "OE1" <-> "OE2" Residue "O GLU 642": "OE1" <-> "OE2" Residue "P GLU 654": "OE1" <-> "OE2" Residue "P GLU 686": "OE1" <-> "OE2" Residue "P GLU 753": "OE1" <-> "OE2" Residue "P GLU 754": "OE1" <-> "OE2" Residue "T GLU 222": "OE1" <-> "OE2" Residue "T GLU 342": "OE1" <-> "OE2" Residue "g TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15250 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1745 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "B" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1758 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain breaks: 1 Chain: "D" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1663 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1794 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain: "M" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1373 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Chain: "N" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1550 Classifications: {'peptide': 187} Link IDs: {'TRANS': 186} Chain breaks: 1 Chain: "O" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1516 Classifications: {'peptide': 178} Link IDs: {'TRANS': 177} Chain breaks: 1 Chain: "P" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1150 Classifications: {'peptide': 138} Link IDs: {'TRANS': 137} Chain breaks: 1 Chain: "T" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1145 Classifications: {'peptide': 137} Link IDs: {'TRANS': 136} Chain breaks: 1 Chain: "g" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1556 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Time building chain proxies: 7.86, per 1000 atoms: 0.52 Number of scatterers: 15250 At special positions: 0 Unit cell: (272.63, 105.49, 319.21, 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 40 16.00 O 2884 8.00 N 2714 7.00 C 9612 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: 6.04 Conformation dependent library (CDL) restraints added in 2.8 seconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 3 sheets defined 77.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 259 through 288 Processing helix chain 'A' and resid 293 through 364 removed outlier: 4.267A pdb=" N PHE A 299 " --> pdb=" O TYR A 295 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 665 removed outlier: 3.824A pdb=" N LYS A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 716 removed outlier: 3.860A pdb=" N PHE A 673 " --> pdb=" O PRO A 669 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 680 " --> pdb=" O TRP A 676 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 704 " --> pdb=" O TRP A 700 " (cutoff:3.500A) Proline residue: A 705 - end of helix removed outlier: 3.539A pdb=" N PHE A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 716 " --> pdb=" O TRP A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 720 removed outlier: 3.740A pdb=" N LYS A 720 " --> pdb=" O GLN A 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 717 through 720' Processing helix chain 'A' and resid 729 through 734 removed outlier: 3.551A pdb=" N ILE A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 729 through 734' Processing helix chain 'B' and resid 254 through 273 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 287 through 361 removed outlier: 3.720A pdb=" N PHE B 293 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN B 294 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 314 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 446 removed outlier: 3.713A pdb=" N ASN B 413 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 438 " --> pdb=" O GLN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.873A pdb=" N ASN B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'D' and resid 264 through 276 removed outlier: 3.511A pdb=" N GLU D 272 " --> pdb=" O GLN D 268 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 304 removed outlier: 3.741A pdb=" N GLU D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D 289 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 4.314A pdb=" N ALA D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE D 297 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 347 removed outlier: 4.079A pdb=" N ILE D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLU D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS D 320 " --> pdb=" O LYS D 316 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN D 325 " --> pdb=" O GLN D 321 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 334 " --> pdb=" O PHE D 330 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU D 347 " --> pdb=" O GLN D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 358 removed outlier: 3.504A pdb=" N PHE D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 394 removed outlier: 5.161A pdb=" N VAL D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG D 384 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 385 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 424 through 453 removed outlier: 3.974A pdb=" N GLN D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS D 445 " --> pdb=" O SER D 441 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA D 446 " --> pdb=" O HIS D 442 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU D 448 " --> pdb=" O VAL D 444 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 260 Processing helix chain 'E' and resid 263 through 290 removed outlier: 3.573A pdb=" N ALA E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN E 270 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Proline residue: E 279 - end of helix Processing helix chain 'E' and resid 296 through 316 removed outlier: 3.763A pdb=" N LEU E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 345 removed outlier: 3.569A pdb=" N LEU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 389 removed outlier: 4.199A pdb=" N GLN E 351 " --> pdb=" O GLU E 347 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN E 360 " --> pdb=" O ASN E 356 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL E 363 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 379 " --> pdb=" O TYR E 375 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU E 381 " --> pdb=" O ASN E 377 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 389 " --> pdb=" O ILE E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 436 removed outlier: 3.624A pdb=" N LYS E 415 " --> pdb=" O ASN E 411 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG E 433 " --> pdb=" O ASN E 429 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 236 removed outlier: 4.100A pdb=" N TYR M 180 " --> pdb=" O ASN M 176 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU M 181 " --> pdb=" O GLU M 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU M 182 " --> pdb=" O LYS M 178 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU M 188 " --> pdb=" O GLN M 184 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG M 189 " --> pdb=" O ALA M 185 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS M 191 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU M 194 " --> pdb=" O GLU M 190 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU M 203 " --> pdb=" O GLU M 199 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU M 210 " --> pdb=" O GLN M 206 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS M 211 " --> pdb=" O GLN M 207 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE M 219 " --> pdb=" O GLN M 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN M 220 " --> pdb=" O ILE M 216 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG M 221 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE M 224 " --> pdb=" O GLN M 220 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS M 229 " --> pdb=" O LYS M 225 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS M 232 " --> pdb=" O ARG M 228 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET M 236 " --> pdb=" O LYS M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 239 No H-bonds generated for 'chain 'M' and resid 237 through 239' Processing helix chain 'M' and resid 240 through 245 removed outlier: 4.521A pdb=" N ARG M 244 " --> pdb=" O GLU M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 255 removed outlier: 3.696A pdb=" N PHE M 253 " --> pdb=" O ASP M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 270 removed outlier: 4.015A pdb=" N LYS M 270 " --> pdb=" O SER M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 294 removed outlier: 3.779A pdb=" N HIS M 292 " --> pdb=" O LEU M 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY M 294 " --> pdb=" O ALA M 290 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 326 removed outlier: 4.446A pdb=" N GLY M 326 " --> pdb=" O TYR M 323 " (cutoff:3.500A) Processing helix chain 'M' and resid 327 through 343 removed outlier: 4.221A pdb=" N ASP M 333 " --> pdb=" O LYS M 329 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE M 335 " --> pdb=" O ALA M 331 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU M 340 " --> pdb=" O ASN M 336 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN M 341 " --> pdb=" O GLY M 337 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 346 No H-bonds generated for 'chain 'M' and resid 344 through 346' Processing helix chain 'N' and resid 566 through 709 removed outlier: 3.850A pdb=" N GLU N 593 " --> pdb=" O SER N 589 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU N 594 " --> pdb=" O SER N 590 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU N 595 " --> pdb=" O LEU N 591 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN N 619 " --> pdb=" O GLU N 615 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU N 632 " --> pdb=" O LYS N 628 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER N 633 " --> pdb=" O LYS N 629 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU N 644 " --> pdb=" O LYS N 640 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU N 645 " --> pdb=" O VAL N 641 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN N 646 " --> pdb=" O PHE N 642 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN N 647 " --> pdb=" O ASN N 643 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN N 656 " --> pdb=" O GLU N 652 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU N 661 " --> pdb=" O GLU N 657 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE N 662 " --> pdb=" O ARG N 658 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU N 679 " --> pdb=" O ALA N 675 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA N 688 " --> pdb=" O ALA N 684 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU N 689 " --> pdb=" O VAL N 685 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS N 700 " --> pdb=" O ASN N 696 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR N 701 " --> pdb=" O LEU N 697 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU N 702 " --> pdb=" O LYS N 698 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER N 703 " --> pdb=" O ILE N 699 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN N 706 " --> pdb=" O GLU N 702 " (cutoff:3.500A) Processing helix chain 'N' and resid 728 through 763 removed outlier: 4.732A pdb=" N ARG N 734 " --> pdb=" O ALA N 730 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU N 735 " --> pdb=" O ALA N 731 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU N 737 " --> pdb=" O GLU N 733 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN N 738 " --> pdb=" O ARG N 734 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS N 740 " --> pdb=" O GLU N 736 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU N 743 " --> pdb=" O ARG N 739 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN N 745 " --> pdb=" O GLY N 741 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA N 746 " --> pdb=" O ASP N 742 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN N 751 " --> pdb=" O LYS N 747 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU N 752 " --> pdb=" O ILE N 748 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN N 760 " --> pdb=" O LYS N 756 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR N 761 " --> pdb=" O ALA N 757 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 620 removed outlier: 3.507A pdb=" N LYS O 549 " --> pdb=" O ILE O 545 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE O 567 " --> pdb=" O ASP O 563 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU O 577 " --> pdb=" O ASN O 573 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP O 583 " --> pdb=" O ASN O 579 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA O 584 " --> pdb=" O LYS O 580 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN O 588 " --> pdb=" O ALA O 584 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS O 589 " --> pdb=" O ILE O 585 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU O 590 " --> pdb=" O TYR O 586 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER O 604 " --> pdb=" O PHE O 600 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU O 616 " --> pdb=" O GLU O 612 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 663 removed outlier: 3.515A pdb=" N LYS O 628 " --> pdb=" O ILE O 624 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU O 629 " --> pdb=" O ASP O 625 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU O 646 " --> pdb=" O GLU O 642 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE O 652 " --> pdb=" O TRP O 648 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN O 653 " --> pdb=" O GLU O 649 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU O 654 " --> pdb=" O ARG O 650 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET O 658 " --> pdb=" O LEU O 654 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA O 661 " --> pdb=" O GLU O 657 " (cutoff:3.500A) Processing helix chain 'O' and resid 670 through 698 removed outlier: 3.668A pdb=" N ASP O 687 " --> pdb=" O LEU O 683 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS O 690 " --> pdb=" O ASP O 686 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS O 691 " --> pdb=" O ASP O 687 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN O 692 " --> pdb=" O LEU O 688 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU O 693 " --> pdb=" O ARG O 689 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE O 696 " --> pdb=" O GLN O 692 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU O 698 " --> pdb=" O ALA O 694 " (cutoff:3.500A) Processing helix chain 'P' and resid 637 through 647 removed outlier: 3.703A pdb=" N LEU P 641 " --> pdb=" O ASP P 637 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR P 647 " --> pdb=" O ILE P 643 " (cutoff:3.500A) Processing helix chain 'P' and resid 647 through 727 removed outlier: 3.853A pdb=" N ARG P 655 " --> pdb=" O LYS P 651 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS P 660 " --> pdb=" O ASN P 656 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS P 661 " --> pdb=" O GLU P 657 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS P 663 " --> pdb=" O LEU P 659 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS P 665 " --> pdb=" O LYS P 661 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY P 685 " --> pdb=" O GLY P 681 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP P 698 " --> pdb=" O ASN P 694 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN P 699 " --> pdb=" O VAL P 695 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS P 717 " --> pdb=" O LYS P 713 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER P 720 " --> pdb=" O ASP P 716 " (cutoff:3.500A) Processing helix chain 'P' and resid 737 through 777 removed outlier: 3.624A pdb=" N LEU P 744 " --> pdb=" O ASP P 740 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR P 746 " --> pdb=" O ARG P 742 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU P 751 " --> pdb=" O ARG P 747 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU P 753 " --> pdb=" O SER P 749 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS P 756 " --> pdb=" O GLU P 752 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET P 765 " --> pdb=" O LYS P 761 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS P 766 " --> pdb=" O LEU P 762 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 225 removed outlier: 3.710A pdb=" N LYS T 218 " --> pdb=" O ILE T 214 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL T 220 " --> pdb=" O ASN T 216 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS T 221 " --> pdb=" O LYS T 217 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP T 225 " --> pdb=" O LYS T 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 228 through 233 Processing helix chain 'T' and resid 235 through 302 removed outlier: 3.647A pdb=" N ARG T 239 " --> pdb=" O ILE T 235 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER T 241 " --> pdb=" O THR T 237 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER T 263 " --> pdb=" O LYS T 259 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN T 264 " --> pdb=" O GLU T 260 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL T 285 " --> pdb=" O SER T 281 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS T 288 " --> pdb=" O LYS T 284 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG T 293 " --> pdb=" O LEU T 289 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS T 294 " --> pdb=" O GLU T 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE T 302 " --> pdb=" O LYS T 298 " (cutoff:3.500A) Processing helix chain 'T' and resid 314 through 339 removed outlier: 3.695A pdb=" N GLN T 325 " --> pdb=" O LYS T 321 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN T 333 " --> pdb=" O TYR T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 355 removed outlier: 3.668A pdb=" N SER T 354 " --> pdb=" O ARG T 350 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 137 through 145 removed outlier: 3.547A pdb=" N ARG g 141 " --> pdb=" O SER g 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 462 through 464 removed outlier: 3.509A pdb=" N VAL B 463 " --> pdb=" O GLN g 133 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG g 164 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS g 81 " --> pdb=" O ILE g 162 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE g 162 " --> pdb=" O LYS g 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'g' and resid 28 through 29 removed outlier: 4.116A pdb=" N GLU g 150 " --> pdb=" O LEU g 94 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN g 92 " --> pdb=" O LEU g 152 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL g 154 " --> pdb=" O GLU g 90 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU g 90 " --> pdb=" O VAL g 154 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N CYS g 119 " --> pdb=" O ARG g 100 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG g 102 " --> pdb=" O CYS g 119 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N MET g 121 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG g 104 " --> pdb=" O MET g 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'g' and resid 32 through 38 removed outlier: 3.710A pdb=" N HIS g 33 " --> pdb=" O MET g 50 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 3021 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: 4.23 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.45: 6276 1.45 - 1.69: 9068 1.69 - 1.92: 74 1.92 - 2.15: 2 2.15 - 2.38: 2 Bond restraints: 15422 Sorted by residual: bond pdb=" CD2 TYR A 295 " pdb=" CE2 TYR A 295 " ideal model delta sigma weight residual 1.382 2.382 -1.000 3.00e-02 1.11e+03 1.11e+03 bond pdb=" CD1 TYR A 295 " pdb=" CE1 TYR A 295 " ideal model delta sigma weight residual 1.382 2.370 -0.988 3.00e-02 1.11e+03 1.08e+03 bond pdb=" CB HIS B 289 " pdb=" CG HIS B 289 " ideal model delta sigma weight residual 1.497 1.913 -0.416 1.40e-02 5.10e+03 8.81e+02 bond pdb=" CE2 TYR A 295 " pdb=" CZ TYR A 295 " ideal model delta sigma weight residual 1.378 2.010 -0.632 2.40e-02 1.74e+03 6.94e+02 bond pdb=" CE1 TYR A 295 " pdb=" CZ TYR A 295 " ideal model delta sigma weight residual 1.378 1.988 -0.610 2.40e-02 1.74e+03 6.47e+02 ... (remaining 15417 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.66: 123 105.66 - 112.77: 8285 112.77 - 119.88: 5474 119.88 - 126.98: 6619 126.98 - 134.09: 82 Bond angle restraints: 20583 Sorted by residual: angle pdb=" CA HIS B 289 " pdb=" CB HIS B 289 " pdb=" CG HIS B 289 " ideal model delta sigma weight residual 113.80 130.66 -16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" ND1 HIS B 289 " pdb=" CG HIS B 289 " pdb=" CD2 HIS B 289 " ideal model delta sigma weight residual 106.10 98.56 7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" C GLU D 308 " pdb=" N GLN D 309 " pdb=" CA GLN D 309 " ideal model delta sigma weight residual 122.61 128.43 -5.82 1.56e+00 4.11e-01 1.39e+01 angle pdb=" CG HIS B 289 " pdb=" CD2 HIS B 289 " pdb=" NE2 HIS B 289 " ideal model delta sigma weight residual 107.20 110.73 -3.53 1.00e+00 1.00e+00 1.25e+01 angle pdb=" C LYS B 275 " pdb=" N LYS B 276 " pdb=" CA LYS B 276 " ideal model delta sigma weight residual 120.90 125.88 -4.98 1.41e+00 5.03e-01 1.25e+01 ... (remaining 20578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8603 17.97 - 35.94: 1016 35.94 - 53.91: 152 53.91 - 71.88: 29 71.88 - 89.85: 31 Dihedral angle restraints: 9831 sinusoidal: 4407 harmonic: 5424 Sorted by residual: dihedral pdb=" CA ALA g 61 " pdb=" C ALA g 61 " pdb=" N PRO g 62 " pdb=" CA PRO g 62 " ideal model delta harmonic sigma weight residual 180.00 141.00 39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA GLU D 307 " pdb=" C GLU D 307 " pdb=" N GLU D 308 " pdb=" CA GLU D 308 " ideal model delta harmonic sigma weight residual 180.00 147.83 32.17 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA LYS E 289 " pdb=" C LYS E 289 " pdb=" N LEU E 290 " pdb=" CA LEU E 290 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 9828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1502 0.034 - 0.068: 595 0.068 - 0.102: 121 0.102 - 0.137: 41 0.137 - 0.171: 10 Chirality restraints: 2269 Sorted by residual: chirality pdb=" CA ILE B 279 " pdb=" N ILE B 279 " pdb=" C ILE B 279 " pdb=" CB ILE B 279 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CG LEU E 307 " pdb=" CB LEU E 307 " pdb=" CD1 LEU E 307 " pdb=" CD2 LEU E 307 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE E 444 " pdb=" N ILE E 444 " pdb=" C ILE E 444 " pdb=" CB ILE E 444 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 2266 not shown) Planarity restraints: 2643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 295 " -0.009 2.00e-02 2.50e+03 3.16e-02 2.00e+01 pdb=" CG TYR A 295 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 295 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 295 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR A 295 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR A 295 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 295 " -0.047 2.00e-02 2.50e+03 pdb=" OH TYR A 295 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA g 61 " -0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO g 62 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO g 62 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO g 62 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 289 " 0.016 2.00e-02 2.50e+03 2.67e-02 1.07e+01 pdb=" CG HIS B 289 " -0.056 2.00e-02 2.50e+03 pdb=" ND1 HIS B 289 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 HIS B 289 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS B 289 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 289 " -0.001 2.00e-02 2.50e+03 ... (remaining 2640 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 197 2.63 - 3.20: 14541 3.20 - 3.77: 23225 3.77 - 4.33: 31270 4.33 - 4.90: 48364 Nonbonded interactions: 117597 Sorted by model distance: nonbonded pdb=" CZ TYR A 295 " pdb=" ND1 HIS B 289 " model vdw 2.065 3.340 nonbonded pdb=" CD2 TYR A 295 " pdb=" CB HIS B 289 " model vdw 2.135 3.740 nonbonded pdb=" CE2 TYR A 295 " pdb=" CB HIS B 289 " model vdw 2.160 3.740 nonbonded pdb=" CE1 TYR A 295 " pdb=" CG HIS B 289 " model vdw 2.163 3.560 nonbonded pdb=" OH TYR N 701 " pdb=" O TRP O 648 " model vdw 2.171 2.440 ... (remaining 117592 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 group one per residue 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: 6.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 28.500 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 40.620 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5092 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 : 0.015 1.000 15422 Z= 1.077 Angle : 0.647 16.857 20583 Z= 0.374 Chirality : 0.039 0.171 2269 Planarity : 0.004 0.084 2643 Dihedral : 15.857 89.849 6267 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.06 % 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: -1.18 (0.20), residues: 1781 helix: -0.30 (0.15), residues: 1256 sheet: -0.14 (0.69), residues: 55 loop : -1.90 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 676 HIS 0.034 0.001 HIS B 289 PHE 0.012 0.001 PHE D 330 TYR 0.055 0.002 TYR A 295 ARG 0.012 0.001 ARG O 689 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 MET cc_start: 0.4753 (mmm) cc_final: 0.4502 (tpt) REVERT: B 473 MET cc_start: -0.0776 (ttt) cc_final: -0.1598 (ttt) REVERT: M 233 SER cc_start: 0.6987 (p) cc_final: 0.6757 (t) REVERT: M 258 TYR cc_start: 0.3359 (p90) cc_final: 0.3043 (t80) REVERT: M 322 ASN cc_start: 0.5994 (p0) cc_final: 0.5666 (p0) REVERT: N 703 SER cc_start: 0.5755 (m) cc_final: 0.5395 (t) REVERT: N 726 TYR cc_start: 0.4467 (m-10) cc_final: 0.4250 (m-80) REVERT: O 576 ASN cc_start: 0.4512 (p0) cc_final: 0.4152 (p0) REVERT: g 90 GLU cc_start: 0.5922 (tt0) cc_final: 0.4954 (tt0) REVERT: g 95 ASP cc_start: 0.5354 (t0) cc_final: 0.5136 (t0) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.3543 time to fit residues: 266.5431 Evaluate side-chains 262 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN B 310 ASN B 442 GLN D 345 GLN D 442 HIS E 300 HIS E 401 GLN E 411 ASN E 416 ASN ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN M 289 GLN N 599 ASN O 519 GLN O 543 GLN ** O 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 644 GLN ** P 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 694 ASN P 710 GLN T 249 GLN g 159 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.998 15422 Z= 1.100 Angle : 0.791 16.496 20583 Z= 0.437 Chirality : 0.045 0.234 2269 Planarity : 0.005 0.078 2643 Dihedral : 5.299 42.539 1960 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 2.82 % Allowed : 15.18 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.11 % 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: -0.70 (0.19), residues: 1781 helix: 0.18 (0.14), residues: 1291 sheet: -0.24 (0.68), residues: 53 loop : -2.20 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 676 HIS 0.033 0.003 HIS B 289 PHE 0.026 0.002 PHE O 606 TYR 0.053 0.003 TYR A 295 ARG 0.009 0.001 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 270 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 MET cc_start: 0.5154 (mtp) cc_final: 0.4950 (mtm) REVERT: B 473 MET cc_start: -0.0551 (ttt) cc_final: -0.1555 (ttt) REVERT: M 258 TYR cc_start: 0.3282 (p90) cc_final: 0.2565 (t80) REVERT: M 263 HIS cc_start: 0.6453 (m90) cc_final: 0.6177 (m90) REVERT: T 293 ARG cc_start: 0.3682 (mmp-170) cc_final: 0.3100 (mmm160) REVERT: g 136 LEU cc_start: 0.8684 (tp) cc_final: 0.8478 (tp) outliers start: 48 outliers final: 27 residues processed: 305 average time/residue: 0.3471 time to fit residues: 143.9746 Evaluate side-chains 220 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 249 ASP Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 661 GLU Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 583 ASP Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 702 ASP Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 97 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 433 ASN B 466 HIS D 289 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 HIS ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 ASN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 519 GLN ** O 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 645 ASN P 694 ASN ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.005 15422 Z= 1.103 Angle : 0.764 16.657 20583 Z= 0.422 Chirality : 0.045 0.234 2269 Planarity : 0.005 0.076 2643 Dihedral : 5.355 46.016 1960 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.44 % Favored : 95.45 % Rotamer: Outliers : 3.82 % Allowed : 19.82 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.11 % 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: -0.56 (0.19), residues: 1781 helix: 0.31 (0.14), residues: 1286 sheet: -0.55 (0.65), residues: 55 loop : -2.22 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 661 HIS 0.035 0.002 HIS B 289 PHE 0.023 0.003 PHE g 184 TYR 0.054 0.003 TYR A 295 ARG 0.007 0.001 ARG M 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 215 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.4629 (OUTLIER) cc_final: 0.4428 (t80) REVERT: B 279 ILE cc_start: 0.4392 (tp) cc_final: 0.4048 (tp) REVERT: B 289 HIS cc_start: 0.3580 (OUTLIER) cc_final: 0.3339 (m90) REVERT: B 319 GLN cc_start: 0.6290 (mm110) cc_final: 0.6071 (mm110) REVERT: B 423 GLU cc_start: 0.5220 (OUTLIER) cc_final: 0.4138 (tm-30) REVERT: B 473 MET cc_start: -0.0433 (ttt) cc_final: -0.1293 (ttt) REVERT: E 307 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6670 (mp) REVERT: M 258 TYR cc_start: 0.3954 (p90) cc_final: 0.2784 (t80) REVERT: M 266 LEU cc_start: 0.1717 (OUTLIER) cc_final: 0.1316 (mm) REVERT: N 568 ASP cc_start: 0.3511 (OUTLIER) cc_final: 0.3253 (m-30) REVERT: O 658 MET cc_start: 0.5645 (tpp) cc_final: 0.5318 (tpp) REVERT: O 681 MET cc_start: 0.3526 (OUTLIER) cc_final: 0.3267 (tpt) outliers start: 65 outliers final: 36 residues processed: 261 average time/residue: 0.3182 time to fit residues: 116.4564 Evaluate side-chains 226 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 249 ASP Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 583 ASP Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 702 ASP Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN E 300 HIS ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.008 15422 Z= 1.094 Angle : 0.713 16.680 20583 Z= 0.396 Chirality : 0.043 0.201 2269 Planarity : 0.005 0.078 2643 Dihedral : 5.244 46.555 1960 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.38 % Favored : 95.51 % Rotamer: Outliers : 4.94 % Allowed : 21.94 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.11 % 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: -0.38 (0.19), residues: 1781 helix: 0.45 (0.14), residues: 1301 sheet: -0.41 (0.74), residues: 48 loop : -2.24 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 661 HIS 0.036 0.002 HIS B 289 PHE 0.027 0.002 PHE O 606 TYR 0.055 0.002 TYR A 295 ARG 0.020 0.001 ARG T 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 212 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.4970 (OUTLIER) cc_final: 0.4632 (m-10) REVERT: A 686 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: A 728 MET cc_start: 0.6911 (pmm) cc_final: 0.6694 (pmm) REVERT: B 279 ILE cc_start: 0.4398 (tp) cc_final: 0.4056 (tp) REVERT: B 289 HIS cc_start: 0.3445 (OUTLIER) cc_final: 0.3181 (m90) REVERT: B 423 GLU cc_start: 0.4996 (OUTLIER) cc_final: 0.4493 (tm-30) REVERT: B 473 MET cc_start: -0.0331 (ttt) cc_final: -0.1129 (ttt) REVERT: D 290 GLU cc_start: 0.3083 (OUTLIER) cc_final: 0.2061 (mt-10) REVERT: D 348 GLU cc_start: 0.6133 (tm-30) cc_final: 0.5883 (tm-30) REVERT: E 300 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.5927 (t-90) REVERT: M 258 TYR cc_start: 0.3820 (p90) cc_final: 0.2862 (t80) REVERT: M 335 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.5733 (mp) REVERT: N 568 ASP cc_start: 0.3509 (OUTLIER) cc_final: 0.3306 (m-30) REVERT: O 658 MET cc_start: 0.5405 (tpp) cc_final: 0.5158 (tpp) REVERT: T 291 LYS cc_start: 0.5058 (ptmm) cc_final: 0.4697 (ptmm) REVERT: T 343 LEU cc_start: 0.5385 (mp) cc_final: 0.5071 (mt) outliers start: 84 outliers final: 48 residues processed: 276 average time/residue: 0.2917 time to fit residues: 115.7274 Evaluate side-chains 232 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 176 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 249 ASP Chi-restraints excluded: chain M residue 287 MET Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 335 ILE Chi-restraints excluded: chain N residue 566 ASN Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 728 ILE Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 583 ASP Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 702 ASP Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 290 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 86 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 666 ASN ** P 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.009 15422 Z= 1.098 Angle : 0.739 16.709 20583 Z= 0.408 Chirality : 0.044 0.271 2269 Planarity : 0.005 0.084 2643 Dihedral : 5.334 46.921 1960 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.55 % Favored : 95.34 % Rotamer: Outliers : 4.71 % Allowed : 23.94 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.06 % 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: -0.48 (0.19), residues: 1781 helix: 0.38 (0.14), residues: 1310 sheet: -0.52 (0.74), residues: 48 loop : -2.32 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP A 661 HIS 0.037 0.003 HIS E 300 PHE 0.022 0.002 PHE g 184 TYR 0.056 0.003 TYR A 295 ARG 0.008 0.001 ARG P 757 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 191 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.4848 (OUTLIER) cc_final: 0.4266 (m-80) REVERT: A 339 GLN cc_start: 0.6162 (OUTLIER) cc_final: 0.5637 (mp10) REVERT: A 686 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6958 (tp30) REVERT: A 708 MET cc_start: 0.4491 (mtt) cc_final: 0.4180 (mtm) REVERT: A 728 MET cc_start: 0.7121 (pmm) cc_final: 0.6917 (pmm) REVERT: B 279 ILE cc_start: 0.4473 (tp) cc_final: 0.4125 (tp) REVERT: B 289 HIS cc_start: 0.3363 (OUTLIER) cc_final: 0.3123 (m90) REVERT: B 473 MET cc_start: -0.0344 (ttt) cc_final: -0.1087 (ttt) REVERT: M 258 TYR cc_start: 0.4098 (p90) cc_final: 0.3172 (t80) REVERT: M 266 LEU cc_start: 0.1500 (OUTLIER) cc_final: 0.1062 (mm) REVERT: M 335 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6117 (mp) REVERT: O 681 MET cc_start: 0.3603 (OUTLIER) cc_final: 0.3085 (tpp) REVERT: T 343 LEU cc_start: 0.5492 (mp) cc_final: 0.5162 (mt) REVERT: g 124 ARG cc_start: 0.5859 (tpp-160) cc_final: 0.5613 (mmt-90) outliers start: 80 outliers final: 55 residues processed: 254 average time/residue: 0.2865 time to fit residues: 104.9966 Evaluate side-chains 236 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 174 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 249 ASP Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 287 MET Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 335 ILE Chi-restraints excluded: chain N residue 566 ASN Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 640 LYS Chi-restraints excluded: chain N residue 700 LYS Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 ILE Chi-restraints excluded: chain N residue 759 ASP Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 583 ASP Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 702 ASP Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 130 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 288 GLN ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 644 GLN ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 710 GLN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.010 15422 Z= 1.095 Angle : 0.727 16.708 20583 Z= 0.402 Chirality : 0.044 0.208 2269 Planarity : 0.005 0.082 2643 Dihedral : 5.300 47.522 1960 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.66 % Favored : 95.23 % Rotamer: Outliers : 5.53 % Allowed : 24.24 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.37 (0.19), residues: 1781 helix: 0.46 (0.14), residues: 1313 sheet: -0.59 (0.75), residues: 48 loop : -2.32 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A 661 HIS 0.036 0.002 HIS B 289 PHE 0.019 0.002 PHE A 685 TYR 0.056 0.002 TYR A 295 ARG 0.008 0.001 ARG P 757 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 196 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.4871 (OUTLIER) cc_final: 0.4312 (m-80) REVERT: A 339 GLN cc_start: 0.6156 (OUTLIER) cc_final: 0.5543 (mp10) REVERT: A 686 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6930 (tp30) REVERT: B 279 ILE cc_start: 0.4763 (tp) cc_final: 0.4513 (tp) REVERT: B 289 HIS cc_start: 0.3161 (OUTLIER) cc_final: 0.2850 (m90) REVERT: B 473 MET cc_start: -0.0295 (ttt) cc_final: -0.0729 (ttt) REVERT: D 348 GLU cc_start: 0.6174 (tm-30) cc_final: 0.5937 (tm-30) REVERT: D 363 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6301 (t80) REVERT: E 300 HIS cc_start: 0.6881 (OUTLIER) cc_final: 0.5995 (t-90) REVERT: M 258 TYR cc_start: 0.4066 (p90) cc_final: 0.3351 (t80) REVERT: M 266 LEU cc_start: 0.1522 (OUTLIER) cc_final: 0.1130 (mm) REVERT: N 758 LEU cc_start: 0.2679 (OUTLIER) cc_final: 0.2296 (tt) REVERT: O 681 MET cc_start: 0.3611 (OUTLIER) cc_final: 0.3057 (tpp) REVERT: T 343 LEU cc_start: 0.5499 (mp) cc_final: 0.5170 (mt) outliers start: 94 outliers final: 64 residues processed: 273 average time/residue: 0.2832 time to fit residues: 112.4570 Evaluate side-chains 246 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 173 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 249 ASP Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 287 MET Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain N residue 566 ASN Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 640 LYS Chi-restraints excluded: chain N residue 700 LYS Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 ILE Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 759 ASP Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 583 ASP Chi-restraints excluded: chain O residue 604 SER Chi-restraints excluded: chain O residue 644 GLN Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 702 ASP Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain T residue 290 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 130 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 644 GLN ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5601 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.008 15422 Z= 1.086 Angle : 0.708 16.661 20583 Z= 0.389 Chirality : 0.043 0.263 2269 Planarity : 0.004 0.081 2643 Dihedral : 5.151 46.431 1960 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.49 % Favored : 95.40 % Rotamer: Outliers : 5.47 % Allowed : 25.06 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.15 (0.20), residues: 1781 helix: 0.64 (0.14), residues: 1310 sheet: -0.57 (0.76), residues: 48 loop : -2.29 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 661 HIS 0.036 0.002 HIS B 289 PHE 0.022 0.002 PHE g 184 TYR 0.057 0.002 TYR A 295 ARG 0.007 0.001 ARG O 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 201 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.4542 (OUTLIER) cc_final: 0.3948 (m-80) REVERT: A 339 GLN cc_start: 0.6028 (OUTLIER) cc_final: 0.5706 (mt0) REVERT: A 656 GLU cc_start: 0.2585 (OUTLIER) cc_final: 0.2298 (tt0) REVERT: A 686 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6891 (tp30) REVERT: B 289 HIS cc_start: 0.3136 (OUTLIER) cc_final: 0.2789 (m90) REVERT: B 473 MET cc_start: 0.0114 (ttt) cc_final: -0.0251 (ttt) REVERT: D 363 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.6316 (t80) REVERT: D 415 LEU cc_start: -0.0866 (OUTLIER) cc_final: -0.1240 (mt) REVERT: M 258 TYR cc_start: 0.3955 (p90) cc_final: 0.3495 (t80) REVERT: M 266 LEU cc_start: 0.1504 (OUTLIER) cc_final: 0.1124 (mm) REVERT: M 322 ASN cc_start: 0.6049 (OUTLIER) cc_final: 0.5840 (p0) REVERT: N 758 LEU cc_start: 0.2544 (OUTLIER) cc_final: 0.2234 (tt) REVERT: O 681 MET cc_start: 0.3505 (OUTLIER) cc_final: 0.2984 (tpp) REVERT: P 736 GLU cc_start: 0.5795 (OUTLIER) cc_final: 0.4913 (tp30) REVERT: T 343 LEU cc_start: 0.5413 (mp) cc_final: 0.5106 (mt) outliers start: 93 outliers final: 63 residues processed: 277 average time/residue: 0.2891 time to fit residues: 116.1335 Evaluate side-chains 255 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 180 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 194 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 249 ASP Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 287 MET Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 322 ASN Chi-restraints excluded: chain N residue 566 ASN Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 661 GLU Chi-restraints excluded: chain N residue 700 LYS Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 ILE Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 759 ASP Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 583 ASP Chi-restraints excluded: chain O residue 604 SER Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain P residue 736 GLU Chi-restraints excluded: chain T residue 290 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 130 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.010 15422 Z= 1.091 Angle : 0.722 16.712 20583 Z= 0.397 Chirality : 0.043 0.219 2269 Planarity : 0.005 0.083 2643 Dihedral : 5.173 46.572 1960 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 5.12 % Allowed : 25.94 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.15 (0.20), residues: 1781 helix: 0.64 (0.14), residues: 1310 sheet: -0.67 (0.76), residues: 48 loop : -2.25 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 661 HIS 0.036 0.003 HIS B 289 PHE 0.016 0.002 PHE A 685 TYR 0.057 0.002 TYR A 295 ARG 0.007 0.001 ARG P 757 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 189 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.4902 (OUTLIER) cc_final: 0.4350 (m-80) REVERT: A 339 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.5704 (mt0) REVERT: A 686 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6896 (tp30) REVERT: B 289 HIS cc_start: 0.3216 (OUTLIER) cc_final: 0.2831 (m90) REVERT: D 363 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6213 (t80) REVERT: D 415 LEU cc_start: -0.0509 (OUTLIER) cc_final: -0.1079 (mt) REVERT: M 223 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7150 (ptmt) REVERT: M 236 MET cc_start: 0.5871 (tmm) cc_final: 0.5466 (ppp) REVERT: M 258 TYR cc_start: 0.3914 (p90) cc_final: 0.3552 (t80) REVERT: M 266 LEU cc_start: 0.1517 (OUTLIER) cc_final: 0.1140 (mm) REVERT: N 758 LEU cc_start: 0.2646 (OUTLIER) cc_final: 0.2272 (tt) REVERT: O 681 MET cc_start: 0.3417 (OUTLIER) cc_final: 0.2969 (tpp) REVERT: P 736 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.4959 (tp30) REVERT: T 343 LEU cc_start: 0.5370 (mp) cc_final: 0.5076 (mt) outliers start: 87 outliers final: 61 residues processed: 256 average time/residue: 0.2784 time to fit residues: 103.6133 Evaluate side-chains 252 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 180 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 194 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 223 LYS Chi-restraints excluded: chain M residue 249 ASP Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 287 MET Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 566 ASN Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 640 LYS Chi-restraints excluded: chain N residue 700 LYS Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 ILE Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 583 ASP Chi-restraints excluded: chain O residue 604 SER Chi-restraints excluded: chain O residue 658 MET Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 702 ASP Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain P residue 736 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 130 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 326 HIS ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 429 ASN ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5661 moved from start: 0.7493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.008 15422 Z= 1.095 Angle : 0.752 16.706 20583 Z= 0.409 Chirality : 0.044 0.218 2269 Planarity : 0.005 0.082 2643 Dihedral : 5.279 47.418 1960 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.66 % Favored : 95.23 % Rotamer: Outliers : 5.29 % Allowed : 25.76 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.28 (0.20), residues: 1781 helix: 0.54 (0.14), residues: 1317 sheet: -0.92 (0.75), residues: 49 loop : -2.28 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 661 HIS 0.036 0.003 HIS B 289 PHE 0.022 0.002 PHE g 184 TYR 0.057 0.002 TYR A 295 ARG 0.006 0.001 ARG P 757 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 188 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.5032 (OUTLIER) cc_final: 0.4322 (m-80) REVERT: A 339 GLN cc_start: 0.5875 (OUTLIER) cc_final: 0.5528 (mt0) REVERT: A 686 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6969 (tp30) REVERT: B 289 HIS cc_start: 0.3301 (OUTLIER) cc_final: 0.2886 (m90) REVERT: D 363 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6335 (t80) REVERT: M 223 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7148 (ptmt) REVERT: M 258 TYR cc_start: 0.3815 (p90) cc_final: 0.3536 (t80) REVERT: M 266 LEU cc_start: 0.1526 (OUTLIER) cc_final: 0.1198 (mm) REVERT: N 758 LEU cc_start: 0.2724 (OUTLIER) cc_final: 0.2322 (tt) REVERT: O 681 MET cc_start: 0.3497 (OUTLIER) cc_final: 0.3038 (tpp) REVERT: P 736 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.4963 (tp30) REVERT: T 343 LEU cc_start: 0.5445 (mp) cc_final: 0.5124 (mt) outliers start: 90 outliers final: 64 residues processed: 254 average time/residue: 0.2796 time to fit residues: 103.2051 Evaluate side-chains 251 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 177 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 194 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 223 LYS Chi-restraints excluded: chain M residue 249 ASP Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 287 MET Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 566 ASN Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 640 LYS Chi-restraints excluded: chain N residue 700 LYS Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 ILE Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 583 ASP Chi-restraints excluded: chain O residue 604 SER Chi-restraints excluded: chain O residue 658 MET Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 696 ARG Chi-restraints excluded: chain P residue 702 ASP Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain P residue 736 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 130 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 160 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 466 HIS ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.7619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.009 15422 Z= 1.081 Angle : 0.718 16.676 20583 Z= 0.393 Chirality : 0.043 0.220 2269 Planarity : 0.004 0.079 2643 Dihedral : 5.047 45.565 1960 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 3.41 % Allowed : 27.71 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1781 helix: 0.73 (0.14), residues: 1309 sheet: -1.09 (0.72), residues: 55 loop : -2.22 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 700 HIS 0.036 0.002 HIS B 289 PHE 0.022 0.001 PHE D 454 TYR 0.056 0.002 TYR A 295 ARG 0.007 0.001 ARG P 757 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 202 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.4913 (OUTLIER) cc_final: 0.4023 (m-80) REVERT: A 339 GLN cc_start: 0.5978 (OUTLIER) cc_final: 0.5718 (mt0) REVERT: A 686 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: B 289 HIS cc_start: 0.2698 (OUTLIER) cc_final: 0.2287 (m90) REVERT: D 415 LEU cc_start: -0.0357 (OUTLIER) cc_final: -0.0826 (mt) REVERT: M 266 LEU cc_start: 0.1571 (OUTLIER) cc_final: 0.1210 (mm) REVERT: N 758 LEU cc_start: 0.2513 (OUTLIER) cc_final: 0.2129 (tt) REVERT: O 681 MET cc_start: 0.3436 (OUTLIER) cc_final: 0.2920 (tpp) REVERT: T 343 LEU cc_start: 0.5410 (mp) cc_final: 0.5101 (mt) outliers start: 58 outliers final: 42 residues processed: 248 average time/residue: 0.2928 time to fit residues: 103.9899 Evaluate side-chains 240 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 190 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 194 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 566 ASN Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 640 LYS Chi-restraints excluded: chain N residue 700 LYS Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 583 ASP Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 130 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.122517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.108167 restraints weight = 69882.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.107054 restraints weight = 62042.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.107533 restraints weight = 54414.330| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.7699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.010 15422 Z= 1.087 Angle : 0.743 16.719 20583 Z= 0.406 Chirality : 0.043 0.215 2269 Planarity : 0.004 0.082 2643 Dihedral : 5.083 45.696 1960 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.38 % Favored : 95.51 % Rotamer: Outliers : 3.71 % Allowed : 27.53 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.11 (0.20), residues: 1781 helix: 0.67 (0.14), residues: 1316 sheet: -0.76 (0.82), residues: 44 loop : -2.28 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 661 HIS 0.036 0.002 HIS B 289 PHE 0.024 0.002 PHE D 454 TYR 0.057 0.002 TYR A 295 ARG 0.006 0.001 ARG E 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3884.39 seconds wall clock time: 71 minutes 2.48 seconds (4262.48 seconds total)