Starting phenix.real_space_refine on Thu Sep 18 19:15:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bbj_7075/09_2025/6bbj_7075.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bbj_7075/09_2025/6bbj_7075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bbj_7075/09_2025/6bbj_7075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bbj_7075/09_2025/6bbj_7075.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bbj_7075/09_2025/6bbj_7075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bbj_7075/09_2025/6bbj_7075.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.037 sd= 0.456 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 124 5.16 5 C 12752 2.51 5 N 3196 2.21 5 O 3424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19496 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4874 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Restraints were copied for chains: B, C, D Time building chain proxies: 4.20, per 1000 atoms: 0.22 Number of scatterers: 19496 At special positions: 0 Unit cell: (142.528, 142.528, 121.856, 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 124 16.00 O 3424 8.00 N 3196 7.00 C 12752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 628.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 64.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.957A pdb=" N LEU A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.823A pdb=" N GLU A 163 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.684A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.818A pdb=" N MET A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 210 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.983A pdb=" N ILE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 3.501A pdb=" N ILE A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.610A pdb=" N GLU A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 252 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.539A pdb=" N ALA A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.061A pdb=" N VAL A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 302 " --> pdb=" O HIS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.644A pdb=" N ALA A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.731A pdb=" N PHE A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 338 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.695A pdb=" N ILE A 361 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 377 removed outlier: 3.898A pdb=" N ALA A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 375 " --> pdb=" O MET A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 387 Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.631A pdb=" N ARG A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS A 397 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 436 removed outlier: 3.640A pdb=" N ILE A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 448 through 486 removed outlier: 3.856A pdb=" N GLU A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 530 removed outlier: 4.514A pdb=" N ARG A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 509 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 510 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 516 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 566 removed outlier: 3.950A pdb=" N LEU A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 561 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 584 removed outlier: 4.509A pdb=" N VAL A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.756A pdb=" N THR A 589 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 590 " --> pdb=" O TYR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 632 removed outlier: 4.088A pdb=" N LEU A 602 " --> pdb=" O TYR A 598 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 605 " --> pdb=" O MET A 601 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 675 removed outlier: 3.700A pdb=" N LYS A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 715 removed outlier: 4.076A pdb=" N ILE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 727 through 744 removed outlier: 3.802A pdb=" N ILE A 737 " --> pdb=" O TRP A 733 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.957A pdb=" N LEU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.823A pdb=" N GLU B 163 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.684A pdb=" N LEU B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.819A pdb=" N MET B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 removed outlier: 3.983A pdb=" N ILE B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 removed outlier: 3.501A pdb=" N ILE B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.610A pdb=" N GLU B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.538A pdb=" N ALA B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 302 removed outlier: 4.061A pdb=" N VAL B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 302 " --> pdb=" O HIS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 327 removed outlier: 3.645A pdb=" N ALA B 323 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 353 removed outlier: 3.731A pdb=" N PHE B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 338 " --> pdb=" O ASN B 334 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.696A pdb=" N ILE B 361 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 377 removed outlier: 3.899A pdb=" N ALA B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 387 Processing helix chain 'B' and resid 392 through 399 removed outlier: 3.632A pdb=" N ARG B 396 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 398 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 removed outlier: 3.641A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 436 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 448 through 486 removed outlier: 3.857A pdb=" N GLU B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 530 removed outlier: 4.514A pdb=" N ARG B 506 " --> pdb=" O MET B 502 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 509 " --> pdb=" O MET B 505 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 510 " --> pdb=" O ARG B 506 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 516 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 566 removed outlier: 3.950A pdb=" N LEU B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 557 " --> pdb=" O SER B 553 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 563 " --> pdb=" O THR B 559 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 584 removed outlier: 4.508A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.756A pdb=" N THR B 589 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 590 " --> pdb=" O TYR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 632 removed outlier: 4.088A pdb=" N LEU B 602 " --> pdb=" O TYR B 598 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 605 " --> pdb=" O MET B 601 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 675 removed outlier: 3.700A pdb=" N LYS B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 715 removed outlier: 4.075A pdb=" N ILE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 709 " --> pdb=" O LEU B 705 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 727 through 744 removed outlier: 3.802A pdb=" N ILE B 737 " --> pdb=" O TRP B 733 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 744 " --> pdb=" O ILE B 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.957A pdb=" N LEU C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER C 155 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.822A pdb=" N GLU C 163 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.684A pdb=" N LEU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 204 through 217 removed outlier: 3.819A pdb=" N MET C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 223 removed outlier: 3.983A pdb=" N ILE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 244 removed outlier: 3.500A pdb=" N ILE C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.611A pdb=" N GLU C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 252 " --> pdb=" O HIS C 248 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 removed outlier: 3.538A pdb=" N ALA C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 302 removed outlier: 4.060A pdb=" N VAL C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C 302 " --> pdb=" O HIS C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.644A pdb=" N ALA C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 353 removed outlier: 3.731A pdb=" N PHE C 337 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 338 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.696A pdb=" N ILE C 361 " --> pdb=" O LEU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 377 removed outlier: 3.898A pdb=" N ALA C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 387 Processing helix chain 'C' and resid 392 through 399 removed outlier: 3.631A pdb=" N ARG C 396 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N HIS C 397 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 436 removed outlier: 3.640A pdb=" N ILE C 432 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 436 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 448 through 486 removed outlier: 3.856A pdb=" N GLU C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL C 465 " --> pdb=" O LYS C 461 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 466 " --> pdb=" O PHE C 462 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 477 " --> pdb=" O SER C 473 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 530 removed outlier: 4.514A pdb=" N ARG C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY C 509 " --> pdb=" O MET C 505 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 510 " --> pdb=" O ARG C 506 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 515 " --> pdb=" O ILE C 511 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 516 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN C 524 " --> pdb=" O PHE C 520 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 525 " --> pdb=" O PHE C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 566 removed outlier: 3.951A pdb=" N LEU C 547 " --> pdb=" O GLY C 543 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 557 " --> pdb=" O SER C 553 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 561 " --> pdb=" O ILE C 557 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 563 " --> pdb=" O THR C 559 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 584 removed outlier: 4.508A pdb=" N VAL C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 582 " --> pdb=" O LEU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 590 removed outlier: 3.756A pdb=" N THR C 589 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG C 590 " --> pdb=" O TYR C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 632 removed outlier: 4.088A pdb=" N LEU C 602 " --> pdb=" O TYR C 598 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 605 " --> pdb=" O MET C 601 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE C 620 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 631 " --> pdb=" O ALA C 627 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 632 " --> pdb=" O LEU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 675 removed outlier: 3.700A pdb=" N LYS C 671 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 672 " --> pdb=" O ASP C 668 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 715 removed outlier: 4.075A pdb=" N ILE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET C 709 " --> pdb=" O LEU C 705 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 710 " --> pdb=" O LEU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 725 Processing helix chain 'C' and resid 727 through 744 removed outlier: 3.802A pdb=" N ILE C 737 " --> pdb=" O TRP C 733 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 744 " --> pdb=" O ILE C 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 157 removed outlier: 3.957A pdb=" N LEU D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER D 155 " --> pdb=" O PHE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.823A pdb=" N GLU D 163 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.685A pdb=" N LEU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 197 Processing helix chain 'D' and resid 204 through 217 removed outlier: 3.819A pdb=" N MET D 208 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 223 removed outlier: 3.984A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.501A pdb=" N ILE D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 removed outlier: 3.610A pdb=" N GLU D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 252 " --> pdb=" O HIS D 248 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 291 removed outlier: 3.538A pdb=" N ALA D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 302 removed outlier: 4.061A pdb=" N VAL D 297 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU D 302 " --> pdb=" O HIS D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.644A pdb=" N ALA D 323 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 353 removed outlier: 3.731A pdb=" N PHE D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL D 338 " --> pdb=" O ASN D 334 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 346 " --> pdb=" O TYR D 342 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 361 removed outlier: 3.695A pdb=" N ILE D 361 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 377 removed outlier: 3.899A pdb=" N ALA D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS D 375 " --> pdb=" O MET D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 387 Processing helix chain 'D' and resid 392 through 399 removed outlier: 3.631A pdb=" N ARG D 396 " --> pdb=" O GLU D 393 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS D 397 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 436 removed outlier: 3.640A pdb=" N ILE D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 448 through 486 removed outlier: 3.856A pdb=" N GLU D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG D 456 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL D 465 " --> pdb=" O LYS D 461 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 466 " --> pdb=" O PHE D 462 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D 481 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 530 removed outlier: 4.514A pdb=" N ARG D 506 " --> pdb=" O MET D 502 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 509 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D 510 " --> pdb=" O ARG D 506 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 515 " --> pdb=" O ILE D 511 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 516 " --> pdb=" O VAL D 512 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN D 524 " --> pdb=" O PHE D 520 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 525 " --> pdb=" O PHE D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 566 removed outlier: 3.950A pdb=" N LEU D 547 " --> pdb=" O GLY D 543 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 557 " --> pdb=" O SER D 553 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 561 " --> pdb=" O ILE D 557 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 563 " --> pdb=" O THR D 559 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 584 removed outlier: 4.509A pdb=" N VAL D 573 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP D 582 " --> pdb=" O LEU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 590 removed outlier: 3.757A pdb=" N THR D 589 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 590 " --> pdb=" O TYR D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 632 removed outlier: 4.088A pdb=" N LEU D 602 " --> pdb=" O TYR D 598 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 605 " --> pdb=" O MET D 601 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 620 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 631 " --> pdb=" O ALA D 627 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 632 " --> pdb=" O LEU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 675 removed outlier: 3.699A pdb=" N LYS D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 715 removed outlier: 4.076A pdb=" N ILE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET D 709 " --> pdb=" O LEU D 705 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 725 Processing helix chain 'D' and resid 727 through 744 removed outlier: 3.801A pdb=" N ILE D 737 " --> pdb=" O TRP D 733 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 744 " --> pdb=" O ILE D 740 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 407 removed outlier: 6.893A pdb=" N SER A 412 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA A 406 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A 771 " --> pdb=" O VAL A 758 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 401 through 407 removed outlier: 6.892A pdb=" N SER B 412 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 406 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 771 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 401 through 407 removed outlier: 6.892A pdb=" N SER C 412 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA C 406 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG C 771 " --> pdb=" O VAL C 758 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 401 through 407 removed outlier: 6.892A pdb=" N SER D 412 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA D 406 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG D 771 " --> pdb=" O VAL D 758 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2472 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: 2.54 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6026 1.34 - 1.46: 4421 1.46 - 1.58: 9261 1.58 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 19924 Sorted by residual: bond pdb=" C GLU C 449 " pdb=" N PRO C 450 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.55e+00 bond pdb=" C GLU D 449 " pdb=" N PRO D 450 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.41e+00 bond pdb=" C GLU A 449 " pdb=" N PRO A 450 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.39e+00 bond pdb=" C GLU B 449 " pdb=" N PRO B 450 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" C ASN D 633 " pdb=" N PRO D 634 " ideal model delta sigma weight residual 1.328 1.344 -0.015 1.26e-02 6.30e+03 1.50e+00 ... (remaining 19919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 26161 1.79 - 3.58: 685 3.58 - 5.37: 82 5.37 - 7.16: 16 7.16 - 8.95: 20 Bond angle restraints: 26964 Sorted by residual: angle pdb=" C GLN B 172 " pdb=" N LYS B 173 " pdb=" CA LYS B 173 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C GLN C 172 " pdb=" N LYS C 173 " pdb=" CA LYS C 173 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C GLN A 172 " pdb=" N LYS A 173 " pdb=" CA LYS A 173 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLN D 172 " pdb=" N LYS D 173 " pdb=" CA LYS D 173 " ideal model delta sigma weight residual 121.54 128.94 -7.40 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C THR B 717 " pdb=" N VAL B 718 " pdb=" CA VAL B 718 " ideal model delta sigma weight residual 122.97 119.28 3.69 9.80e-01 1.04e+00 1.42e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.65: 10638 9.65 - 19.30: 966 19.30 - 28.95: 124 28.95 - 38.59: 52 38.59 - 48.24: 40 Dihedral angle restraints: 11820 sinusoidal: 4688 harmonic: 7132 Sorted by residual: dihedral pdb=" CA VAL A 561 " pdb=" C VAL A 561 " pdb=" N LEU A 562 " pdb=" CA LEU A 562 " ideal model delta harmonic sigma weight residual 180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA VAL C 561 " pdb=" C VAL C 561 " pdb=" N LEU C 562 " pdb=" CA LEU C 562 " ideal model delta harmonic sigma weight residual -180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA VAL B 561 " pdb=" C VAL B 561 " pdb=" N LEU B 562 " pdb=" CA LEU B 562 " ideal model delta harmonic sigma weight residual -180.00 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 11817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1985 0.038 - 0.076: 907 0.076 - 0.113: 168 0.113 - 0.151: 40 0.151 - 0.189: 8 Chirality restraints: 3108 Sorted by residual: chirality pdb=" CA GLU C 449 " pdb=" N GLU C 449 " pdb=" C GLU C 449 " pdb=" CB GLU C 449 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA GLU B 449 " pdb=" N GLU B 449 " pdb=" C GLU B 449 " pdb=" CB GLU B 449 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA GLU A 449 " pdb=" N GLU A 449 " pdb=" C GLU A 449 " pdb=" CB GLU A 449 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 3105 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 408 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO B 409 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 408 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 409 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 408 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 409 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 409 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 409 " 0.023 5.00e-02 4.00e+02 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 6558 2.87 - 3.37: 18485 3.37 - 3.88: 30936 3.88 - 4.39: 35137 4.39 - 4.90: 58888 Nonbonded interactions: 150004 Sorted by model distance: nonbonded pdb=" O ASP A 152 " pdb=" OG SER A 155 " model vdw 2.358 3.040 nonbonded pdb=" O ASP B 152 " pdb=" OG SER B 155 " model vdw 2.358 3.040 nonbonded pdb=" O ASP D 152 " pdb=" OG SER D 155 " model vdw 2.358 3.040 nonbonded pdb=" O ASP C 152 " pdb=" OG SER C 155 " model vdw 2.359 3.040 nonbonded pdb=" O PHE C 467 " pdb=" OG SER C 470 " model vdw 2.361 3.040 ... (remaining 149999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.430 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 0.003 0.044 19924 Z= 0.164 Angle : 0.726 8.951 26964 Z= 0.403 Chirality : 0.044 0.189 3108 Planarity : 0.005 0.042 3324 Dihedral : 8.257 48.242 7220 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.19 % Allowed : 1.33 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.00 (0.12), residues: 2400 helix: -3.84 (0.07), residues: 1284 sheet: -2.85 (0.47), residues: 84 loop : -2.42 (0.16), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 387 TYR 0.028 0.002 TYR B 687 PHE 0.017 0.002 PHE C 337 TRP 0.010 0.002 TRP C 772 HIS 0.008 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00348 (19924) covalent geometry : angle 0.72610 (26964) hydrogen bonds : bond 0.31355 ( 852) hydrogen bonds : angle 9.64524 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 927 time to evaluate : 0.685 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: A 186 THR cc_start: 0.8206 (p) cc_final: 0.7872 (t) REVERT: A 209 LEU cc_start: 0.8924 (mt) cc_final: 0.8704 (mt) REVERT: A 222 PHE cc_start: 0.7200 (t80) cc_final: 0.6179 (t80) REVERT: A 381 ILE cc_start: 0.8922 (tp) cc_final: 0.8631 (mm) REVERT: A 584 ASN cc_start: 0.8751 (m-40) cc_final: 0.8531 (m110) REVERT: A 615 LEU cc_start: 0.9206 (mt) cc_final: 0.8398 (tp) REVERT: A 619 LEU cc_start: 0.9376 (mt) cc_final: 0.9018 (mt) REVERT: A 630 SER cc_start: 0.9082 (m) cc_final: 0.8798 (p) REVERT: B 181 PHE cc_start: 0.7510 (m-80) cc_final: 0.7240 (m-80) REVERT: B 186 THR cc_start: 0.8152 (p) cc_final: 0.7798 (t) REVERT: B 209 LEU cc_start: 0.8951 (mt) cc_final: 0.8701 (mt) REVERT: B 222 PHE cc_start: 0.7381 (t80) cc_final: 0.6172 (t80) REVERT: B 299 TYR cc_start: 0.7972 (t80) cc_final: 0.7742 (t80) REVERT: B 381 ILE cc_start: 0.8914 (tp) cc_final: 0.8613 (mm) REVERT: B 393 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 584 ASN cc_start: 0.8894 (m-40) cc_final: 0.8629 (m110) REVERT: B 615 LEU cc_start: 0.9223 (mt) cc_final: 0.8460 (tp) REVERT: B 619 LEU cc_start: 0.9354 (mt) cc_final: 0.9089 (mt) REVERT: B 630 SER cc_start: 0.9129 (m) cc_final: 0.8868 (p) REVERT: C 181 PHE cc_start: 0.7452 (m-80) cc_final: 0.7202 (m-80) REVERT: C 186 THR cc_start: 0.8073 (p) cc_final: 0.7721 (t) REVERT: C 209 LEU cc_start: 0.8939 (mt) cc_final: 0.8673 (mt) REVERT: C 222 PHE cc_start: 0.7364 (t80) cc_final: 0.6205 (t80) REVERT: C 381 ILE cc_start: 0.8896 (tp) cc_final: 0.8688 (mm) REVERT: C 615 LEU cc_start: 0.9241 (mt) cc_final: 0.9024 (mt) REVERT: C 630 SER cc_start: 0.9418 (m) cc_final: 0.9164 (p) REVERT: C 693 ILE cc_start: 0.8944 (pt) cc_final: 0.8688 (tp) REVERT: D 181 PHE cc_start: 0.7695 (m-80) cc_final: 0.7393 (m-80) REVERT: D 186 THR cc_start: 0.7978 (p) cc_final: 0.7615 (t) REVERT: D 209 LEU cc_start: 0.8977 (mt) cc_final: 0.8733 (mt) REVERT: D 222 PHE cc_start: 0.7569 (t80) cc_final: 0.6318 (t80) REVERT: D 299 TYR cc_start: 0.8151 (t80) cc_final: 0.7936 (t80) REVERT: D 381 ILE cc_start: 0.8865 (tp) cc_final: 0.8615 (mm) REVERT: D 387 ARG cc_start: 0.8300 (mpp80) cc_final: 0.7987 (mtm-85) REVERT: D 393 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7590 (mm-30) REVERT: D 520 PHE cc_start: 0.8808 (t80) cc_final: 0.8594 (t80) REVERT: D 522 ILE cc_start: 0.8845 (mm) cc_final: 0.8630 (tp) REVERT: D 584 ASN cc_start: 0.9118 (m-40) cc_final: 0.8806 (m110) REVERT: D 615 LEU cc_start: 0.9152 (mt) cc_final: 0.8555 (tp) REVERT: D 619 LEU cc_start: 0.9381 (mt) cc_final: 0.9157 (mt) REVERT: D 630 SER cc_start: 0.9301 (m) cc_final: 0.9080 (p) REVERT: D 667 LEU cc_start: 0.8684 (tp) cc_final: 0.8440 (tp) outliers start: 4 outliers final: 0 residues processed: 931 average time/residue: 0.1335 time to fit residues: 189.4219 Evaluate side-chains 528 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.0670 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 239 HIS ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 239 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN C 203 ASN C 239 HIS ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 727 GLN D 203 ASN D 239 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 727 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.079855 restraints weight = 51639.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.082377 restraints weight = 25688.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084012 restraints weight = 15547.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085124 restraints weight = 10718.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085898 restraints weight = 8118.997| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19924 Z= 0.138 Angle : 0.622 7.692 26964 Z= 0.324 Chirality : 0.041 0.155 3108 Planarity : 0.004 0.041 3324 Dihedral : 4.355 15.406 2656 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.84 % Allowed : 13.80 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.73 (0.15), residues: 2400 helix: -1.64 (0.11), residues: 1416 sheet: -1.40 (0.52), residues: 76 loop : -1.90 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 456 TYR 0.020 0.002 TYR D 232 PHE 0.024 0.002 PHE A 545 TRP 0.017 0.001 TRP C 772 HIS 0.006 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00299 (19924) covalent geometry : angle 0.62236 (26964) hydrogen bonds : bond 0.05497 ( 852) hydrogen bonds : angle 4.77302 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 596 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8199 (mm-30) REVERT: A 186 THR cc_start: 0.8107 (p) cc_final: 0.7794 (t) REVERT: A 423 CYS cc_start: 0.7020 (t) cc_final: 0.6284 (p) REVERT: A 459 TRP cc_start: 0.8771 (t-100) cc_final: 0.8475 (t-100) REVERT: A 520 PHE cc_start: 0.8639 (t80) cc_final: 0.8349 (t80) REVERT: A 553 SER cc_start: 0.9665 (m) cc_final: 0.9242 (p) REVERT: A 609 ASP cc_start: 0.7900 (m-30) cc_final: 0.7199 (t70) REVERT: A 614 LEU cc_start: 0.9215 (tp) cc_final: 0.8952 (tp) REVERT: A 615 LEU cc_start: 0.9063 (mt) cc_final: 0.8571 (tp) REVERT: A 703 PHE cc_start: 0.8865 (t80) cc_final: 0.8507 (t80) REVERT: A 709 MET cc_start: 0.8732 (mmt) cc_final: 0.8475 (mmt) REVERT: B 186 THR cc_start: 0.8167 (p) cc_final: 0.7860 (t) REVERT: B 459 TRP cc_start: 0.8748 (t-100) cc_final: 0.8461 (t-100) REVERT: B 520 PHE cc_start: 0.8688 (t80) cc_final: 0.8345 (t80) REVERT: B 553 SER cc_start: 0.9660 (m) cc_final: 0.9255 (p) REVERT: B 609 ASP cc_start: 0.7955 (m-30) cc_final: 0.7248 (t70) REVERT: B 614 LEU cc_start: 0.9214 (tp) cc_final: 0.9006 (tp) REVERT: B 615 LEU cc_start: 0.9032 (mt) cc_final: 0.8546 (tp) REVERT: B 619 LEU cc_start: 0.9303 (mt) cc_final: 0.9098 (mt) REVERT: B 703 PHE cc_start: 0.8857 (t80) cc_final: 0.8518 (t80) REVERT: B 709 MET cc_start: 0.8766 (mmt) cc_final: 0.8499 (mmt) REVERT: C 186 THR cc_start: 0.8067 (p) cc_final: 0.7780 (t) REVERT: C 283 LEU cc_start: 0.9142 (mm) cc_final: 0.8852 (mm) REVERT: C 423 CYS cc_start: 0.6870 (t) cc_final: 0.6642 (p) REVERT: C 520 PHE cc_start: 0.9091 (t80) cc_final: 0.8400 (t80) REVERT: C 553 SER cc_start: 0.9714 (m) cc_final: 0.9274 (p) REVERT: C 584 ASN cc_start: 0.8801 (m110) cc_final: 0.8177 (m110) REVERT: C 609 ASP cc_start: 0.7976 (m-30) cc_final: 0.7270 (t70) REVERT: C 703 PHE cc_start: 0.8927 (t80) cc_final: 0.8631 (t80) REVERT: D 186 THR cc_start: 0.7996 (p) cc_final: 0.7698 (t) REVERT: D 243 GLU cc_start: 0.8245 (tp30) cc_final: 0.7969 (tp30) REVERT: D 520 PHE cc_start: 0.8924 (t80) cc_final: 0.8498 (t80) REVERT: D 553 SER cc_start: 0.9668 (m) cc_final: 0.9257 (p) REVERT: D 609 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7422 (t70) REVERT: D 615 LEU cc_start: 0.9026 (mt) cc_final: 0.8669 (tp) REVERT: D 618 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.9016 (mm) REVERT: D 628 LEU cc_start: 0.9119 (mt) cc_final: 0.8853 (mm) REVERT: D 665 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8490 (t80) REVERT: D 668 ASP cc_start: 0.7909 (m-30) cc_final: 0.6803 (m-30) REVERT: D 676 MET cc_start: 0.7396 (mtp) cc_final: 0.7183 (mtm) REVERT: D 698 TYR cc_start: 0.8573 (t80) cc_final: 0.8098 (t80) outliers start: 81 outliers final: 37 residues processed: 644 average time/residue: 0.1209 time to fit residues: 123.9364 Evaluate side-chains 507 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 467 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 665 PHE Chi-restraints excluded: chain D residue 678 ASP Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 777 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 155 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 121 optimal weight: 0.0570 chunk 179 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 305 HIS ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN D 305 HIS ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076940 restraints weight = 52156.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079386 restraints weight = 25910.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080991 restraints weight = 15703.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.082081 restraints weight = 10857.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.082788 restraints weight = 8235.191| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19924 Z= 0.134 Angle : 0.602 10.509 26964 Z= 0.303 Chirality : 0.041 0.232 3108 Planarity : 0.003 0.031 3324 Dihedral : 4.209 14.898 2656 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 5.41 % Allowed : 16.60 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.16), residues: 2400 helix: -0.43 (0.13), residues: 1372 sheet: -1.49 (0.49), residues: 76 loop : -1.60 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 456 TYR 0.019 0.002 TYR D 299 PHE 0.016 0.002 PHE B 168 TRP 0.014 0.001 TRP C 459 HIS 0.005 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00306 (19924) covalent geometry : angle 0.60207 (26964) hydrogen bonds : bond 0.04025 ( 852) hydrogen bonds : angle 4.14757 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 532 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8012 (p) cc_final: 0.7733 (t) REVERT: A 208 MET cc_start: 0.8293 (mmp) cc_final: 0.8027 (mmm) REVERT: A 283 LEU cc_start: 0.9112 (mm) cc_final: 0.8846 (mm) REVERT: A 423 CYS cc_start: 0.6898 (t) cc_final: 0.6687 (p) REVERT: A 507 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8222 (mt) REVERT: A 614 LEU cc_start: 0.9271 (tp) cc_final: 0.9034 (tp) REVERT: A 615 LEU cc_start: 0.8954 (mt) cc_final: 0.8736 (tp) REVERT: A 621 MET cc_start: 0.8999 (mmt) cc_final: 0.8588 (mmt) REVERT: A 628 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8228 (mm) REVERT: A 665 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8431 (t80) REVERT: A 694 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8911 (mm) REVERT: A 703 PHE cc_start: 0.8970 (t80) cc_final: 0.8649 (t80) REVERT: A 727 GLN cc_start: 0.7111 (pt0) cc_final: 0.6659 (pm20) REVERT: A 750 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8207 (mmtt) REVERT: A 772 TRP cc_start: 0.8469 (m100) cc_final: 0.8151 (m100) REVERT: B 154 VAL cc_start: 0.9239 (m) cc_final: 0.8908 (p) REVERT: B 186 THR cc_start: 0.8020 (p) cc_final: 0.7753 (t) REVERT: B 283 LEU cc_start: 0.9079 (mm) cc_final: 0.8810 (mm) REVERT: B 427 VAL cc_start: 0.8192 (p) cc_final: 0.7983 (m) REVERT: B 553 SER cc_start: 0.9599 (m) cc_final: 0.9198 (p) REVERT: B 609 ASP cc_start: 0.8011 (m-30) cc_final: 0.7535 (t0) REVERT: B 614 LEU cc_start: 0.9295 (tp) cc_final: 0.9094 (tp) REVERT: B 615 LEU cc_start: 0.8899 (mt) cc_final: 0.8534 (tp) REVERT: B 628 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8200 (mm) REVERT: B 665 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8429 (t80) REVERT: B 694 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8879 (mm) REVERT: B 698 TYR cc_start: 0.8588 (t80) cc_final: 0.8238 (t80) REVERT: B 703 PHE cc_start: 0.8984 (t80) cc_final: 0.8625 (t80) REVERT: B 727 GLN cc_start: 0.7080 (pt0) cc_final: 0.6589 (pm20) REVERT: B 772 TRP cc_start: 0.8462 (m100) cc_final: 0.8154 (m100) REVERT: C 154 VAL cc_start: 0.9312 (m) cc_final: 0.8990 (p) REVERT: C 186 THR cc_start: 0.7958 (p) cc_final: 0.7713 (t) REVERT: C 283 LEU cc_start: 0.9167 (mm) cc_final: 0.8834 (mm) REVERT: C 520 PHE cc_start: 0.9132 (t80) cc_final: 0.8613 (t80) REVERT: C 553 SER cc_start: 0.9659 (m) cc_final: 0.9257 (p) REVERT: C 571 LEU cc_start: 0.9275 (tp) cc_final: 0.8879 (tt) REVERT: C 584 ASN cc_start: 0.8782 (m110) cc_final: 0.8196 (m110) REVERT: C 609 ASP cc_start: 0.8003 (m-30) cc_final: 0.7606 (t0) REVERT: C 615 LEU cc_start: 0.9158 (mt) cc_final: 0.8868 (tp) REVERT: C 628 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8622 (mm) REVERT: C 668 ASP cc_start: 0.8216 (m-30) cc_final: 0.7087 (m-30) REVERT: C 698 TYR cc_start: 0.8703 (t80) cc_final: 0.8288 (t80) REVERT: C 703 PHE cc_start: 0.8967 (t80) cc_final: 0.8716 (t80) REVERT: C 706 LEU cc_start: 0.8834 (mt) cc_final: 0.8461 (tp) REVERT: C 777 ASP cc_start: 0.8248 (m-30) cc_final: 0.8023 (m-30) REVERT: D 151 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7730 (t80) REVERT: D 186 THR cc_start: 0.7903 (p) cc_final: 0.7602 (t) REVERT: D 208 MET cc_start: 0.8210 (mmp) cc_final: 0.7932 (mmm) REVERT: D 283 LEU cc_start: 0.9142 (mm) cc_final: 0.8833 (mm) REVERT: D 520 PHE cc_start: 0.8870 (t80) cc_final: 0.8623 (t80) REVERT: D 553 SER cc_start: 0.9583 (m) cc_final: 0.9208 (p) REVERT: D 609 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7737 (t0) REVERT: D 615 LEU cc_start: 0.9075 (mt) cc_final: 0.8736 (tp) REVERT: D 621 MET cc_start: 0.8977 (mmt) cc_final: 0.8608 (mmt) REVERT: D 628 LEU cc_start: 0.9238 (mt) cc_final: 0.9008 (mm) REVERT: D 676 MET cc_start: 0.7469 (mtp) cc_final: 0.7265 (mtm) REVERT: D 694 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8953 (mm) REVERT: D 698 TYR cc_start: 0.8578 (t80) cc_final: 0.8194 (t80) REVERT: D 703 PHE cc_start: 0.8897 (t80) cc_final: 0.8655 (t80) REVERT: D 727 GLN cc_start: 0.7057 (pt0) cc_final: 0.6648 (pm20) outliers start: 114 outliers final: 47 residues processed: 603 average time/residue: 0.1203 time to fit residues: 115.8589 Evaluate side-chains 527 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 469 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 681 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 678 ASP Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 11 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 GLN ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076828 restraints weight = 51657.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079248 restraints weight = 25510.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080820 restraints weight = 15431.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.081895 restraints weight = 10688.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.082621 restraints weight = 8129.234| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19924 Z= 0.124 Angle : 0.579 13.118 26964 Z= 0.292 Chirality : 0.040 0.158 3108 Planarity : 0.003 0.030 3324 Dihedral : 4.128 16.636 2656 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.79 % Allowed : 18.22 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.17), residues: 2400 helix: 0.16 (0.13), residues: 1356 sheet: -1.23 (0.51), residues: 76 loop : -1.27 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 267 TYR 0.015 0.001 TYR D 563 PHE 0.021 0.001 PHE B 520 TRP 0.012 0.001 TRP D 459 HIS 0.005 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00285 (19924) covalent geometry : angle 0.57905 (26964) hydrogen bonds : bond 0.03519 ( 852) hydrogen bonds : angle 3.85096 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 522 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.7916 (p) cc_final: 0.7672 (t) REVERT: A 283 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8899 (mm) REVERT: A 301 THR cc_start: 0.8845 (p) cc_final: 0.8601 (p) REVERT: A 478 MET cc_start: 0.8286 (tpp) cc_final: 0.8061 (tpp) REVERT: A 503 ASP cc_start: 0.7717 (m-30) cc_final: 0.7381 (m-30) REVERT: A 504 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: A 507 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8330 (mt) REVERT: A 553 SER cc_start: 0.9565 (m) cc_final: 0.9223 (p) REVERT: A 609 ASP cc_start: 0.7934 (m-30) cc_final: 0.7491 (t0) REVERT: A 614 LEU cc_start: 0.9258 (tp) cc_final: 0.9005 (tp) REVERT: A 615 LEU cc_start: 0.8981 (mt) cc_final: 0.8752 (tp) REVERT: A 665 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8510 (t80) REVERT: A 694 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8870 (mm) REVERT: A 727 GLN cc_start: 0.7055 (pt0) cc_final: 0.6690 (pm20) REVERT: A 750 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8188 (mmtt) REVERT: B 146 ASN cc_start: 0.7314 (p0) cc_final: 0.6969 (p0) REVERT: B 154 VAL cc_start: 0.9217 (m) cc_final: 0.8918 (p) REVERT: B 186 THR cc_start: 0.7944 (p) cc_final: 0.7716 (t) REVERT: B 243 GLU cc_start: 0.8243 (tp30) cc_final: 0.7724 (tp30) REVERT: B 283 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8927 (mm) REVERT: B 553 SER cc_start: 0.9573 (m) cc_final: 0.9199 (p) REVERT: B 609 ASP cc_start: 0.7967 (m-30) cc_final: 0.7531 (t0) REVERT: B 615 LEU cc_start: 0.8892 (mt) cc_final: 0.8647 (tp) REVERT: B 621 MET cc_start: 0.8933 (mmp) cc_final: 0.8566 (mmt) REVERT: B 665 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8551 (t80) REVERT: B 672 LEU cc_start: 0.9306 (mt) cc_final: 0.9102 (mm) REVERT: B 694 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8847 (mm) REVERT: B 698 TYR cc_start: 0.8579 (t80) cc_final: 0.8228 (t80) REVERT: B 727 GLN cc_start: 0.7097 (pt0) cc_final: 0.6692 (pm20) REVERT: C 146 ASN cc_start: 0.7324 (p0) cc_final: 0.6968 (p0) REVERT: C 186 THR cc_start: 0.7904 (p) cc_final: 0.7674 (t) REVERT: C 263 GLN cc_start: 0.7719 (mt0) cc_final: 0.7331 (mt0) REVERT: C 283 LEU cc_start: 0.9180 (mm) cc_final: 0.8926 (mm) REVERT: C 483 LEU cc_start: 0.9233 (mp) cc_final: 0.9021 (mp) REVERT: C 507 LEU cc_start: 0.8834 (tp) cc_final: 0.8478 (mt) REVERT: C 520 PHE cc_start: 0.9110 (t80) cc_final: 0.8651 (t80) REVERT: C 553 SER cc_start: 0.9694 (m) cc_final: 0.9284 (p) REVERT: C 571 LEU cc_start: 0.9276 (tp) cc_final: 0.8880 (tt) REVERT: C 584 ASN cc_start: 0.8779 (m110) cc_final: 0.8154 (m110) REVERT: C 609 ASP cc_start: 0.7955 (m-30) cc_final: 0.7323 (t0) REVERT: C 615 LEU cc_start: 0.9136 (mt) cc_final: 0.8910 (tp) REVERT: C 698 TYR cc_start: 0.8666 (t80) cc_final: 0.8258 (t80) REVERT: C 703 PHE cc_start: 0.8992 (t80) cc_final: 0.8671 (t80) REVERT: C 709 MET cc_start: 0.8599 (mmt) cc_final: 0.8199 (mmt) REVERT: D 151 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7656 (t80) REVERT: D 186 THR cc_start: 0.7851 (p) cc_final: 0.7617 (t) REVERT: D 283 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8845 (mm) REVERT: D 301 THR cc_start: 0.8755 (p) cc_final: 0.8494 (p) REVERT: D 520 PHE cc_start: 0.8879 (t80) cc_final: 0.8611 (t80) REVERT: D 553 SER cc_start: 0.9562 (m) cc_final: 0.9205 (p) REVERT: D 609 ASP cc_start: 0.8087 (m-30) cc_final: 0.7584 (t0) REVERT: D 615 LEU cc_start: 0.9108 (mt) cc_final: 0.8838 (tp) REVERT: D 676 MET cc_start: 0.7622 (mtp) cc_final: 0.7402 (mtm) REVERT: D 698 TYR cc_start: 0.8592 (t80) cc_final: 0.8263 (t80) REVERT: D 700 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8796 (tt) REVERT: D 703 PHE cc_start: 0.8921 (t80) cc_final: 0.8481 (t80) REVERT: D 727 GLN cc_start: 0.7117 (pt0) cc_final: 0.6791 (pm20) outliers start: 101 outliers final: 52 residues processed: 585 average time/residue: 0.1111 time to fit residues: 106.2440 Evaluate side-chains 542 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 479 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 727 GLN Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 205 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 31 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 0.0670 chunk 215 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN C 199 ASN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 727 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.090179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078363 restraints weight = 51818.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.080714 restraints weight = 25568.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.082309 restraints weight = 15664.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.083376 restraints weight = 10848.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.084106 restraints weight = 8265.875| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19924 Z= 0.109 Angle : 0.568 12.740 26964 Z= 0.283 Chirality : 0.039 0.222 3108 Planarity : 0.003 0.031 3324 Dihedral : 3.983 15.232 2656 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.22 % Allowed : 19.50 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.17), residues: 2400 helix: 0.54 (0.14), residues: 1364 sheet: -1.71 (0.50), residues: 84 loop : -1.07 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 267 TYR 0.015 0.001 TYR D 563 PHE 0.017 0.001 PHE B 181 TRP 0.012 0.001 TRP C 729 HIS 0.004 0.001 HIS A 443 Details of bonding type rmsd covalent geometry : bond 0.00250 (19924) covalent geometry : angle 0.56762 (26964) hydrogen bonds : bond 0.03211 ( 852) hydrogen bonds : angle 3.61952 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 533 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 186 THR cc_start: 0.7941 (p) cc_final: 0.7712 (t) REVERT: A 208 MET cc_start: 0.8251 (mmp) cc_final: 0.7971 (mmm) REVERT: A 283 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 367 MET cc_start: 0.7815 (mmm) cc_final: 0.7048 (mmm) REVERT: A 449 GLU cc_start: 0.7808 (tp30) cc_final: 0.7499 (tp30) REVERT: A 503 ASP cc_start: 0.7741 (m-30) cc_final: 0.7429 (m-30) REVERT: A 504 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: A 507 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8453 (mt) REVERT: A 541 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7638 (mm) REVERT: A 553 SER cc_start: 0.9516 (m) cc_final: 0.9183 (p) REVERT: A 609 ASP cc_start: 0.7976 (m-30) cc_final: 0.7552 (t0) REVERT: A 614 LEU cc_start: 0.9249 (tp) cc_final: 0.9026 (tp) REVERT: A 615 LEU cc_start: 0.8993 (mt) cc_final: 0.8759 (tp) REVERT: A 694 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8810 (mm) REVERT: A 727 GLN cc_start: 0.7096 (pt0) cc_final: 0.6599 (pm20) REVERT: B 186 THR cc_start: 0.7939 (p) cc_final: 0.7691 (t) REVERT: B 498 TYR cc_start: 0.6483 (m-10) cc_final: 0.6219 (m-10) REVERT: B 541 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7655 (mm) REVERT: B 553 SER cc_start: 0.9546 (m) cc_final: 0.9207 (p) REVERT: B 558 ILE cc_start: 0.9489 (mt) cc_final: 0.9257 (mm) REVERT: B 609 ASP cc_start: 0.7907 (m-30) cc_final: 0.7490 (t0) REVERT: B 615 LEU cc_start: 0.8914 (mt) cc_final: 0.8708 (tp) REVERT: B 726 LYS cc_start: 0.7793 (mmtp) cc_final: 0.7488 (mmmm) REVERT: B 727 GLN cc_start: 0.7149 (pt0) cc_final: 0.6636 (pm20) REVERT: C 186 THR cc_start: 0.7980 (p) cc_final: 0.7717 (t) REVERT: C 263 GLN cc_start: 0.7687 (mt0) cc_final: 0.7106 (mt0) REVERT: C 283 LEU cc_start: 0.9091 (mm) cc_final: 0.8715 (mm) REVERT: C 453 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7768 (mm-30) REVERT: C 483 LEU cc_start: 0.9186 (mp) cc_final: 0.8955 (mp) REVERT: C 507 LEU cc_start: 0.8900 (tp) cc_final: 0.8669 (mt) REVERT: C 520 PHE cc_start: 0.9097 (t80) cc_final: 0.8621 (t80) REVERT: C 553 SER cc_start: 0.9629 (m) cc_final: 0.9212 (p) REVERT: C 571 LEU cc_start: 0.9226 (tp) cc_final: 0.8930 (tt) REVERT: C 609 ASP cc_start: 0.7918 (m-30) cc_final: 0.7515 (t0) REVERT: C 615 LEU cc_start: 0.9121 (mt) cc_final: 0.8868 (tp) REVERT: C 628 LEU cc_start: 0.9189 (mm) cc_final: 0.8959 (mp) REVERT: C 698 TYR cc_start: 0.8658 (t80) cc_final: 0.8267 (t80) REVERT: C 703 PHE cc_start: 0.9011 (t80) cc_final: 0.8638 (t80) REVERT: C 739 ASP cc_start: 0.7612 (t0) cc_final: 0.7366 (t0) REVERT: D 151 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7566 (t80) REVERT: D 186 THR cc_start: 0.7910 (p) cc_final: 0.7629 (t) REVERT: D 283 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8802 (mm) REVERT: D 520 PHE cc_start: 0.8821 (t80) cc_final: 0.8475 (t80) REVERT: D 541 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7630 (mm) REVERT: D 553 SER cc_start: 0.9503 (m) cc_final: 0.9195 (p) REVERT: D 609 ASP cc_start: 0.7981 (m-30) cc_final: 0.7563 (t0) REVERT: D 615 LEU cc_start: 0.9031 (mt) cc_final: 0.8804 (tp) REVERT: D 694 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9143 (mm) REVERT: D 698 TYR cc_start: 0.8570 (t80) cc_final: 0.8102 (t80) REVERT: D 700 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8817 (tt) REVERT: D 703 PHE cc_start: 0.8875 (t80) cc_final: 0.8519 (t80) REVERT: D 706 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8503 (tp) REVERT: D 709 MET cc_start: 0.8537 (mmp) cc_final: 0.8289 (mmt) REVERT: D 726 LYS cc_start: 0.7692 (mmtm) cc_final: 0.7393 (mmmm) REVERT: D 727 GLN cc_start: 0.7179 (pt0) cc_final: 0.6740 (pm20) outliers start: 89 outliers final: 50 residues processed: 593 average time/residue: 0.1133 time to fit residues: 109.7347 Evaluate side-chains 533 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 471 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 678 ASP Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 777 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 167 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 210 optimal weight: 0.0980 chunk 4 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 293 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 GLN ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.090234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078109 restraints weight = 52277.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.080509 restraints weight = 26413.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.082082 restraints weight = 16283.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.083126 restraints weight = 11435.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.083879 restraints weight = 8852.678| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19924 Z= 0.112 Angle : 0.585 13.741 26964 Z= 0.289 Chirality : 0.040 0.155 3108 Planarity : 0.003 0.041 3324 Dihedral : 3.946 16.226 2656 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.22 % Allowed : 19.69 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.17), residues: 2400 helix: 0.77 (0.14), residues: 1360 sheet: -1.65 (0.49), residues: 84 loop : -0.86 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 267 TYR 0.016 0.001 TYR D 563 PHE 0.023 0.001 PHE B 280 TRP 0.013 0.001 TRP D 459 HIS 0.004 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00262 (19924) covalent geometry : angle 0.58548 (26964) hydrogen bonds : bond 0.03128 ( 852) hydrogen bonds : angle 3.58437 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 505 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 THR cc_start: 0.8023 (p) cc_final: 0.7754 (t) REVERT: A 283 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 302 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8573 (pp20) REVERT: A 503 ASP cc_start: 0.7855 (m-30) cc_final: 0.7577 (m-30) REVERT: A 504 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: A 507 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8494 (mt) REVERT: A 541 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7720 (mm) REVERT: A 553 SER cc_start: 0.9502 (m) cc_final: 0.9120 (p) REVERT: A 609 ASP cc_start: 0.7874 (m-30) cc_final: 0.7404 (t0) REVERT: A 614 LEU cc_start: 0.9289 (tp) cc_final: 0.9052 (tp) REVERT: A 615 LEU cc_start: 0.8950 (mt) cc_final: 0.8722 (tp) REVERT: A 665 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8465 (t80) REVERT: A 726 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7462 (mmmm) REVERT: A 727 GLN cc_start: 0.7138 (pt0) cc_final: 0.6632 (pm20) REVERT: B 186 THR cc_start: 0.8086 (p) cc_final: 0.7827 (t) REVERT: B 222 PHE cc_start: 0.6916 (t80) cc_final: 0.6671 (t80) REVERT: B 383 GLN cc_start: 0.8789 (mt0) cc_final: 0.8532 (mm-40) REVERT: B 541 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7741 (mm) REVERT: B 553 SER cc_start: 0.9531 (m) cc_final: 0.9176 (p) REVERT: B 609 ASP cc_start: 0.7865 (m-30) cc_final: 0.7349 (t0) REVERT: B 665 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8499 (t80) REVERT: B 709 MET cc_start: 0.8650 (mmt) cc_final: 0.8412 (mmt) REVERT: B 726 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7574 (mmmm) REVERT: B 727 GLN cc_start: 0.7152 (pt0) cc_final: 0.6673 (pm20) REVERT: C 222 PHE cc_start: 0.7328 (t80) cc_final: 0.7011 (t80) REVERT: C 263 GLN cc_start: 0.7807 (mt0) cc_final: 0.7439 (mt0) REVERT: C 283 LEU cc_start: 0.9079 (mm) cc_final: 0.8719 (mm) REVERT: C 367 MET cc_start: 0.7412 (mmm) cc_final: 0.7120 (mmm) REVERT: C 453 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7732 (mm-30) REVERT: C 483 LEU cc_start: 0.9122 (mp) cc_final: 0.8916 (mp) REVERT: C 504 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: C 507 LEU cc_start: 0.8934 (tp) cc_final: 0.8623 (mt) REVERT: C 520 PHE cc_start: 0.9022 (t80) cc_final: 0.8625 (t80) REVERT: C 571 LEU cc_start: 0.9286 (tp) cc_final: 0.9036 (tt) REVERT: C 609 ASP cc_start: 0.7919 (m-30) cc_final: 0.7460 (t0) REVERT: C 615 LEU cc_start: 0.9078 (mt) cc_final: 0.8851 (tp) REVERT: C 628 LEU cc_start: 0.9186 (mm) cc_final: 0.8978 (mp) REVERT: C 703 PHE cc_start: 0.9021 (t80) cc_final: 0.8667 (t80) REVERT: C 739 ASP cc_start: 0.7572 (t0) cc_final: 0.7313 (t0) REVERT: D 151 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7642 (t80) REVERT: D 186 THR cc_start: 0.8009 (p) cc_final: 0.7751 (t) REVERT: D 283 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8786 (mm) REVERT: D 367 MET cc_start: 0.8162 (mmm) cc_final: 0.5623 (mmm) REVERT: D 520 PHE cc_start: 0.8824 (t80) cc_final: 0.8426 (t80) REVERT: D 541 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7656 (mm) REVERT: D 553 SER cc_start: 0.9521 (m) cc_final: 0.9152 (p) REVERT: D 609 ASP cc_start: 0.7961 (m-30) cc_final: 0.7516 (t0) REVERT: D 694 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9180 (mm) REVERT: D 698 TYR cc_start: 0.8479 (t80) cc_final: 0.8102 (t80) REVERT: D 700 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8701 (tt) REVERT: D 703 PHE cc_start: 0.8863 (t80) cc_final: 0.8478 (t80) REVERT: D 709 MET cc_start: 0.8513 (mmp) cc_final: 0.8168 (mmt) REVERT: D 727 GLN cc_start: 0.7202 (pt0) cc_final: 0.6761 (pm20) outliers start: 110 outliers final: 67 residues processed: 580 average time/residue: 0.1097 time to fit residues: 103.9852 Evaluate side-chains 548 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 467 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 678 ASP Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 163 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 222 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 263 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 GLN C 197 ASN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075404 restraints weight = 52044.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.077741 restraints weight = 25994.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079277 restraints weight = 15909.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.080311 restraints weight = 11137.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.081039 restraints weight = 8575.183| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19924 Z= 0.149 Angle : 0.610 10.683 26964 Z= 0.306 Chirality : 0.041 0.143 3108 Planarity : 0.003 0.041 3324 Dihedral : 4.035 16.137 2656 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.55 % Allowed : 20.40 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2400 helix: 0.86 (0.14), residues: 1376 sheet: -1.15 (0.49), residues: 76 loop : -0.81 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 267 TYR 0.019 0.001 TYR D 563 PHE 0.026 0.002 PHE B 280 TRP 0.016 0.001 TRP D 459 HIS 0.011 0.001 HIS C 443 Details of bonding type rmsd covalent geometry : bond 0.00355 (19924) covalent geometry : angle 0.60973 (26964) hydrogen bonds : bond 0.03185 ( 852) hydrogen bonds : angle 3.62657 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 460 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 186 THR cc_start: 0.7966 (p) cc_final: 0.7677 (t) REVERT: A 282 GLU cc_start: 0.7718 (tt0) cc_final: 0.7297 (pt0) REVERT: A 283 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8751 (mm) REVERT: A 302 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8659 (pp20) REVERT: A 431 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7241 (mm-30) REVERT: A 503 ASP cc_start: 0.7849 (m-30) cc_final: 0.7559 (m-30) REVERT: A 504 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: A 507 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8471 (mt) REVERT: A 541 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7913 (mm) REVERT: A 553 SER cc_start: 0.9560 (m) cc_final: 0.9188 (p) REVERT: A 609 ASP cc_start: 0.7965 (m-30) cc_final: 0.7621 (t0) REVERT: A 614 LEU cc_start: 0.9350 (tp) cc_final: 0.9124 (tp) REVERT: A 615 LEU cc_start: 0.9058 (mt) cc_final: 0.8791 (tp) REVERT: A 628 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8440 (mm) REVERT: A 665 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8540 (t80) REVERT: A 716 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7499 (mt-10) REVERT: A 726 LYS cc_start: 0.7688 (mmtm) cc_final: 0.7434 (mmmm) REVERT: A 727 GLN cc_start: 0.7221 (pt0) cc_final: 0.6734 (pm20) REVERT: B 186 THR cc_start: 0.8061 (p) cc_final: 0.7852 (t) REVERT: B 222 PHE cc_start: 0.6988 (t80) cc_final: 0.6747 (t80) REVERT: B 541 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7948 (mm) REVERT: B 553 SER cc_start: 0.9626 (m) cc_final: 0.9211 (p) REVERT: B 573 VAL cc_start: 0.9463 (OUTLIER) cc_final: 0.9262 (t) REVERT: B 609 ASP cc_start: 0.7930 (m-30) cc_final: 0.7524 (t0) REVERT: B 665 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8563 (t80) REVERT: B 709 MET cc_start: 0.8649 (mmt) cc_final: 0.8424 (mmt) REVERT: B 726 LYS cc_start: 0.7768 (mmtp) cc_final: 0.7563 (mmmm) REVERT: B 727 GLN cc_start: 0.7396 (pt0) cc_final: 0.6843 (pm20) REVERT: C 222 PHE cc_start: 0.7310 (t80) cc_final: 0.6991 (t80) REVERT: C 263 GLN cc_start: 0.7810 (mt0) cc_final: 0.7392 (mt0) REVERT: C 283 LEU cc_start: 0.9097 (mm) cc_final: 0.8852 (mm) REVERT: C 453 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7670 (mm-30) REVERT: C 483 LEU cc_start: 0.9153 (mp) cc_final: 0.8936 (mp) REVERT: C 504 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: C 507 LEU cc_start: 0.8989 (tp) cc_final: 0.8633 (mt) REVERT: C 520 PHE cc_start: 0.9020 (t80) cc_final: 0.8591 (t80) REVERT: C 553 SER cc_start: 0.9704 (m) cc_final: 0.9280 (p) REVERT: C 571 LEU cc_start: 0.9314 (tp) cc_final: 0.8940 (tt) REVERT: C 609 ASP cc_start: 0.7989 (m-30) cc_final: 0.7705 (t0) REVERT: C 615 LEU cc_start: 0.9155 (mt) cc_final: 0.8840 (tp) REVERT: C 628 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8894 (mp) REVERT: C 727 GLN cc_start: 0.7542 (pm20) cc_final: 0.7109 (pm20) REVERT: C 739 ASP cc_start: 0.7557 (t0) cc_final: 0.7302 (t0) REVERT: D 151 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7733 (t80) REVERT: D 186 THR cc_start: 0.7986 (p) cc_final: 0.7712 (t) REVERT: D 283 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8773 (mm) REVERT: D 431 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7211 (mm-30) REVERT: D 503 ASP cc_start: 0.8319 (m-30) cc_final: 0.7932 (t0) REVERT: D 520 PHE cc_start: 0.8906 (t80) cc_final: 0.8482 (t80) REVERT: D 541 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7824 (mm) REVERT: D 553 SER cc_start: 0.9578 (m) cc_final: 0.9214 (p) REVERT: D 609 ASP cc_start: 0.8004 (m-30) cc_final: 0.7537 (t0) REVERT: D 615 LEU cc_start: 0.9265 (tp) cc_final: 0.9000 (tt) REVERT: D 631 LEU cc_start: 0.9089 (mp) cc_final: 0.8762 (mp) REVERT: D 698 TYR cc_start: 0.8577 (t80) cc_final: 0.8258 (t80) REVERT: D 700 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8757 (tt) REVERT: D 703 PHE cc_start: 0.8873 (t80) cc_final: 0.8536 (t80) REVERT: D 706 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8627 (tp) REVERT: D 709 MET cc_start: 0.8561 (mmp) cc_final: 0.8235 (mmt) REVERT: D 726 LYS cc_start: 0.7685 (mmtm) cc_final: 0.7482 (mmmm) REVERT: D 727 GLN cc_start: 0.7389 (pt0) cc_final: 0.6922 (pm20) outliers start: 117 outliers final: 79 residues processed: 531 average time/residue: 0.1165 time to fit residues: 101.6195 Evaluate side-chains 540 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 444 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 443 HIS Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 678 ASP Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 GLN B 218 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.074656 restraints weight = 52133.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076991 restraints weight = 26262.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078531 restraints weight = 16194.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079557 restraints weight = 11394.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080300 restraints weight = 8848.334| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19924 Z= 0.144 Angle : 0.615 12.038 26964 Z= 0.308 Chirality : 0.041 0.186 3108 Planarity : 0.003 0.038 3324 Dihedral : 4.062 16.302 2656 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.65 % Allowed : 21.16 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2400 helix: 0.86 (0.14), residues: 1396 sheet: -1.71 (0.48), residues: 84 loop : -0.77 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 267 TYR 0.020 0.001 TYR D 563 PHE 0.023 0.001 PHE B 280 TRP 0.020 0.001 TRP D 459 HIS 0.009 0.001 HIS C 443 Details of bonding type rmsd covalent geometry : bond 0.00343 (19924) covalent geometry : angle 0.61514 (26964) hydrogen bonds : bond 0.03151 ( 852) hydrogen bonds : angle 3.62753 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 453 time to evaluate : 0.823 Fit side-chains REVERT: A 302 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8615 (pp20) REVERT: A 503 ASP cc_start: 0.7889 (m-30) cc_final: 0.7624 (m-30) REVERT: A 504 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: A 507 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 541 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7961 (mm) REVERT: A 553 SER cc_start: 0.9530 (m) cc_final: 0.9186 (p) REVERT: A 609 ASP cc_start: 0.7927 (m-30) cc_final: 0.7520 (t0) REVERT: A 614 LEU cc_start: 0.9353 (tp) cc_final: 0.9149 (tp) REVERT: A 615 LEU cc_start: 0.9075 (mt) cc_final: 0.8803 (tp) REVERT: A 628 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8485 (mm) REVERT: A 665 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8560 (t80) REVERT: A 716 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7519 (mt-10) REVERT: A 726 LYS cc_start: 0.7688 (mmtm) cc_final: 0.7444 (mmmm) REVERT: A 727 GLN cc_start: 0.7270 (pt0) cc_final: 0.7012 (pt0) REVERT: A 742 ARG cc_start: 0.8673 (mmt90) cc_final: 0.8391 (mmm-85) REVERT: B 263 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8116 (tp-100) REVERT: B 371 MET cc_start: 0.8760 (ptp) cc_final: 0.8539 (ptp) REVERT: B 541 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7964 (mm) REVERT: B 609 ASP cc_start: 0.7921 (m-30) cc_final: 0.7536 (t0) REVERT: B 628 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8569 (mm) REVERT: B 665 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8591 (t80) REVERT: B 709 MET cc_start: 0.8562 (mmt) cc_final: 0.8339 (mmt) REVERT: B 716 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 727 GLN cc_start: 0.7400 (pt0) cc_final: 0.7087 (pt0) REVERT: C 222 PHE cc_start: 0.7289 (t80) cc_final: 0.6975 (t80) REVERT: C 263 GLN cc_start: 0.7861 (mt0) cc_final: 0.7519 (mt0) REVERT: C 283 LEU cc_start: 0.9074 (mm) cc_final: 0.8849 (mm) REVERT: C 453 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7688 (mm-30) REVERT: C 504 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.8154 (m-80) REVERT: C 507 LEU cc_start: 0.9058 (tp) cc_final: 0.8689 (mt) REVERT: C 520 PHE cc_start: 0.9000 (t80) cc_final: 0.8595 (t80) REVERT: C 553 SER cc_start: 0.9696 (m) cc_final: 0.9281 (p) REVERT: C 609 ASP cc_start: 0.7985 (m-30) cc_final: 0.7654 (t0) REVERT: C 615 LEU cc_start: 0.9158 (mt) cc_final: 0.8848 (tp) REVERT: C 628 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8861 (mp) REVERT: C 727 GLN cc_start: 0.7551 (pm20) cc_final: 0.7091 (pm20) REVERT: C 739 ASP cc_start: 0.7533 (t0) cc_final: 0.7300 (t0) REVERT: D 151 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7767 (t80) REVERT: D 283 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8783 (mm) REVERT: D 367 MET cc_start: 0.8148 (mmm) cc_final: 0.7771 (mmm) REVERT: D 431 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7190 (mm-30) REVERT: D 503 ASP cc_start: 0.8306 (m-30) cc_final: 0.7934 (t0) REVERT: D 504 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: D 520 PHE cc_start: 0.8906 (t80) cc_final: 0.8497 (t80) REVERT: D 541 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7885 (mm) REVERT: D 553 SER cc_start: 0.9556 (m) cc_final: 0.9206 (p) REVERT: D 609 ASP cc_start: 0.7882 (m-30) cc_final: 0.7403 (t0) REVERT: D 694 LEU cc_start: 0.9451 (mm) cc_final: 0.9215 (mm) REVERT: D 698 TYR cc_start: 0.8581 (t80) cc_final: 0.8248 (t80) REVERT: D 700 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8757 (tt) REVERT: D 703 PHE cc_start: 0.8875 (t80) cc_final: 0.8534 (t80) REVERT: D 706 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8645 (tp) REVERT: D 709 MET cc_start: 0.8458 (mmp) cc_final: 0.8249 (mmt) REVERT: D 727 GLN cc_start: 0.7402 (pt0) cc_final: 0.6955 (pm20) outliers start: 119 outliers final: 82 residues processed: 527 average time/residue: 0.1156 time to fit residues: 98.7832 Evaluate side-chains 533 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 434 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 443 HIS Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 504 TYR Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 678 ASP Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 38 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 239 optimal weight: 6.9990 chunk 139 optimal weight: 0.0570 chunk 11 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 298 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 GLN B 263 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.086422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.074271 restraints weight = 51713.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076593 restraints weight = 26073.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.078116 restraints weight = 16070.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079125 restraints weight = 11312.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079855 restraints weight = 8807.009| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19924 Z= 0.151 Angle : 0.649 12.739 26964 Z= 0.321 Chirality : 0.043 0.288 3108 Planarity : 0.004 0.039 3324 Dihedral : 4.104 16.935 2656 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.12 % Allowed : 22.25 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2400 helix: 0.87 (0.14), residues: 1388 sheet: -1.79 (0.45), residues: 88 loop : -0.76 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 267 TYR 0.021 0.001 TYR D 563 PHE 0.024 0.001 PHE B 280 TRP 0.027 0.002 TRP B 459 HIS 0.009 0.001 HIS C 443 Details of bonding type rmsd covalent geometry : bond 0.00361 (19924) covalent geometry : angle 0.64902 (26964) hydrogen bonds : bond 0.03224 ( 852) hydrogen bonds : angle 3.74328 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 454 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8582 (pp20) REVERT: A 431 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7451 (tm-30) REVERT: A 503 ASP cc_start: 0.8042 (m-30) cc_final: 0.7777 (m-30) REVERT: A 504 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: A 507 LEU cc_start: 0.8898 (mt) cc_final: 0.8469 (mt) REVERT: A 541 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8003 (mm) REVERT: A 553 SER cc_start: 0.9548 (m) cc_final: 0.9234 (p) REVERT: A 609 ASP cc_start: 0.7963 (m-30) cc_final: 0.7617 (t0) REVERT: A 615 LEU cc_start: 0.9090 (mt) cc_final: 0.8818 (tp) REVERT: A 628 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8475 (mm) REVERT: A 665 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8574 (t80) REVERT: A 716 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7515 (mt-10) REVERT: A 726 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7483 (mmmm) REVERT: A 727 GLN cc_start: 0.7336 (pt0) cc_final: 0.7031 (pt0) REVERT: B 263 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7622 (tp-100) REVERT: B 282 GLU cc_start: 0.7434 (pt0) cc_final: 0.6772 (pt0) REVERT: B 283 LEU cc_start: 0.9030 (mm) cc_final: 0.8747 (mm) REVERT: B 371 MET cc_start: 0.8689 (ptp) cc_final: 0.8329 (ptp) REVERT: B 387 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.7855 (ptp90) REVERT: B 431 GLU cc_start: 0.7946 (tp30) cc_final: 0.7585 (tp30) REVERT: B 490 MET cc_start: 0.7808 (mtm) cc_final: 0.7363 (mpp) REVERT: B 503 ASP cc_start: 0.8267 (m-30) cc_final: 0.8025 (t0) REVERT: B 504 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: B 520 PHE cc_start: 0.9035 (t80) cc_final: 0.8614 (t80) REVERT: B 541 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8014 (mm) REVERT: B 553 SER cc_start: 0.9627 (m) cc_final: 0.9264 (p) REVERT: B 609 ASP cc_start: 0.7938 (m-30) cc_final: 0.7521 (t0) REVERT: B 628 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8635 (mm) REVERT: B 665 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8594 (t80) REVERT: B 709 MET cc_start: 0.8579 (mmt) cc_final: 0.8364 (mmt) REVERT: B 716 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7346 (mt-10) REVERT: B 727 GLN cc_start: 0.7426 (pt0) cc_final: 0.7115 (pt0) REVERT: C 222 PHE cc_start: 0.7261 (t80) cc_final: 0.6894 (t80) REVERT: C 263 GLN cc_start: 0.7894 (mt0) cc_final: 0.7543 (mt0) REVERT: C 283 LEU cc_start: 0.9075 (mm) cc_final: 0.8857 (mm) REVERT: C 453 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7690 (mm-30) REVERT: C 504 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: C 507 LEU cc_start: 0.9071 (tp) cc_final: 0.8860 (mt) REVERT: C 520 PHE cc_start: 0.9004 (t80) cc_final: 0.8641 (t80) REVERT: C 553 SER cc_start: 0.9683 (m) cc_final: 0.9267 (p) REVERT: C 609 ASP cc_start: 0.8019 (m-30) cc_final: 0.7715 (t0) REVERT: C 615 LEU cc_start: 0.9142 (mt) cc_final: 0.8851 (tp) REVERT: C 628 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8818 (mp) REVERT: C 631 LEU cc_start: 0.8827 (mp) cc_final: 0.8573 (mp) REVERT: C 727 GLN cc_start: 0.7610 (pm20) cc_final: 0.7168 (pm20) REVERT: C 739 ASP cc_start: 0.7615 (t0) cc_final: 0.7355 (t0) REVERT: D 151 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7760 (t80) REVERT: D 367 MET cc_start: 0.8302 (mmm) cc_final: 0.8052 (mmm) REVERT: D 431 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7275 (mm-30) REVERT: D 503 ASP cc_start: 0.8335 (m-30) cc_final: 0.7983 (t0) REVERT: D 504 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: D 520 PHE cc_start: 0.8894 (t80) cc_final: 0.8494 (t80) REVERT: D 541 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7938 (mm) REVERT: D 553 SER cc_start: 0.9554 (m) cc_final: 0.9216 (p) REVERT: D 609 ASP cc_start: 0.7851 (m-30) cc_final: 0.7400 (t0) REVERT: D 631 LEU cc_start: 0.9159 (mt) cc_final: 0.8727 (tt) REVERT: D 694 LEU cc_start: 0.9443 (mm) cc_final: 0.9220 (mm) REVERT: D 698 TYR cc_start: 0.8608 (t80) cc_final: 0.8257 (t80) REVERT: D 700 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8756 (tt) REVERT: D 703 PHE cc_start: 0.8887 (t80) cc_final: 0.8548 (t80) REVERT: D 716 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7603 (mt-10) REVERT: D 727 GLN cc_start: 0.7469 (pt0) cc_final: 0.7040 (pm20) outliers start: 108 outliers final: 83 residues processed: 520 average time/residue: 0.1215 time to fit residues: 102.7452 Evaluate side-chains 530 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 431 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 443 HIS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 504 TYR Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 GLN B 263 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.087180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075058 restraints weight = 51504.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077410 restraints weight = 25740.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078964 restraints weight = 15759.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.079997 restraints weight = 11007.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.080757 restraints weight = 8498.071| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19924 Z= 0.132 Angle : 0.660 13.372 26964 Z= 0.320 Chirality : 0.043 0.373 3108 Planarity : 0.003 0.036 3324 Dihedral : 4.063 18.089 2656 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.84 % Allowed : 22.72 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.17), residues: 2400 helix: 0.90 (0.14), residues: 1388 sheet: -1.72 (0.44), residues: 88 loop : -0.73 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 267 TYR 0.021 0.001 TYR D 563 PHE 0.020 0.001 PHE B 280 TRP 0.026 0.002 TRP B 459 HIS 0.008 0.001 HIS C 443 Details of bonding type rmsd covalent geometry : bond 0.00317 (19924) covalent geometry : angle 0.65961 (26964) hydrogen bonds : bond 0.03189 ( 852) hydrogen bonds : angle 3.70225 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 451 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8534 (pp20) REVERT: A 431 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7457 (tm-30) REVERT: A 503 ASP cc_start: 0.8059 (m-30) cc_final: 0.7832 (m-30) REVERT: A 504 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: A 507 LEU cc_start: 0.8897 (mt) cc_final: 0.8488 (mt) REVERT: A 541 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7964 (mm) REVERT: A 553 SER cc_start: 0.9542 (m) cc_final: 0.9207 (p) REVERT: A 609 ASP cc_start: 0.7958 (m-30) cc_final: 0.7602 (t0) REVERT: A 615 LEU cc_start: 0.9079 (mt) cc_final: 0.8837 (tp) REVERT: A 628 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8434 (mm) REVERT: A 665 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8560 (t80) REVERT: A 716 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7547 (mt-10) REVERT: A 726 LYS cc_start: 0.7756 (mmtm) cc_final: 0.7527 (mmmm) REVERT: A 727 GLN cc_start: 0.7313 (pt0) cc_final: 0.7041 (pt0) REVERT: B 263 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7758 (tp-100) REVERT: B 283 LEU cc_start: 0.8974 (mm) cc_final: 0.8731 (mm) REVERT: B 371 MET cc_start: 0.8646 (ptp) cc_final: 0.8376 (ptp) REVERT: B 431 GLU cc_start: 0.8005 (tp30) cc_final: 0.7632 (tp30) REVERT: B 478 MET cc_start: 0.7745 (tpp) cc_final: 0.7475 (tpp) REVERT: B 504 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: B 520 PHE cc_start: 0.9001 (t80) cc_final: 0.8622 (t80) REVERT: B 541 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7983 (mm) REVERT: B 553 SER cc_start: 0.9569 (m) cc_final: 0.9249 (p) REVERT: B 609 ASP cc_start: 0.7987 (m-30) cc_final: 0.7554 (t0) REVERT: B 628 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8612 (mm) REVERT: B 665 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8585 (t80) REVERT: B 709 MET cc_start: 0.8540 (mmt) cc_final: 0.8331 (mmt) REVERT: B 716 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 727 GLN cc_start: 0.7410 (pt0) cc_final: 0.7088 (pt0) REVERT: C 263 GLN cc_start: 0.7906 (mt0) cc_final: 0.7577 (mt0) REVERT: C 283 LEU cc_start: 0.9063 (mm) cc_final: 0.8852 (mm) REVERT: C 453 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7663 (mm-30) REVERT: C 504 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: C 520 PHE cc_start: 0.9044 (t80) cc_final: 0.8666 (t80) REVERT: C 553 SER cc_start: 0.9682 (m) cc_final: 0.9266 (p) REVERT: C 609 ASP cc_start: 0.8021 (m-30) cc_final: 0.7718 (t0) REVERT: C 615 LEU cc_start: 0.9126 (mt) cc_final: 0.8876 (tp) REVERT: C 628 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8861 (mp) REVERT: C 631 LEU cc_start: 0.8924 (mp) cc_final: 0.8716 (mp) REVERT: C 703 PHE cc_start: 0.9029 (t80) cc_final: 0.8686 (t80) REVERT: C 727 GLN cc_start: 0.7577 (pm20) cc_final: 0.7228 (pm20) REVERT: C 739 ASP cc_start: 0.7604 (t0) cc_final: 0.7354 (t0) REVERT: D 151 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7704 (t80) REVERT: D 367 MET cc_start: 0.8221 (mmm) cc_final: 0.7393 (mmm) REVERT: D 431 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7254 (mm-30) REVERT: D 503 ASP cc_start: 0.8345 (m-30) cc_final: 0.7999 (t0) REVERT: D 504 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: D 520 PHE cc_start: 0.8889 (t80) cc_final: 0.8480 (t80) REVERT: D 541 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7857 (mm) REVERT: D 553 SER cc_start: 0.9546 (m) cc_final: 0.9210 (p) REVERT: D 609 ASP cc_start: 0.7999 (m-30) cc_final: 0.7647 (t0) REVERT: D 631 LEU cc_start: 0.9210 (mt) cc_final: 0.8788 (tt) REVERT: D 694 LEU cc_start: 0.9425 (mm) cc_final: 0.9194 (mm) REVERT: D 698 TYR cc_start: 0.8589 (t80) cc_final: 0.8225 (t80) REVERT: D 700 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8724 (tt) REVERT: D 703 PHE cc_start: 0.8861 (t80) cc_final: 0.8508 (t80) REVERT: D 716 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7657 (mt-10) REVERT: D 727 GLN cc_start: 0.7441 (pt0) cc_final: 0.6986 (pm20) outliers start: 102 outliers final: 76 residues processed: 515 average time/residue: 0.1218 time to fit residues: 102.7770 Evaluate side-chains 527 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 435 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 443 HIS Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 443 HIS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 504 TYR Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 203 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 217 optimal weight: 0.0770 chunk 87 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 GLN B 263 GLN B 293 GLN B 298 HIS ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076785 restraints weight = 51452.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079149 restraints weight = 25661.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080707 restraints weight = 15673.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.081779 restraints weight = 10938.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.082471 restraints weight = 8388.445| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19924 Z= 0.118 Angle : 0.657 13.723 26964 Z= 0.315 Chirality : 0.043 0.392 3108 Planarity : 0.003 0.037 3324 Dihedral : 4.024 22.360 2656 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.13 % Allowed : 24.24 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2400 helix: 0.94 (0.14), residues: 1392 sheet: -1.61 (0.41), residues: 108 loop : -0.65 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 267 TYR 0.021 0.001 TYR D 563 PHE 0.019 0.001 PHE A 222 TRP 0.024 0.001 TRP B 459 HIS 0.007 0.001 HIS C 443 Details of bonding type rmsd covalent geometry : bond 0.00276 (19924) covalent geometry : angle 0.65719 (26964) hydrogen bonds : bond 0.03077 ( 852) hydrogen bonds : angle 3.64062 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3303.33 seconds wall clock time: 57 minutes 47.92 seconds (3467.92 seconds total)