Starting phenix.real_space_refine on Fri Mar 6 18:40:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wbb_32396/03_2026/7wbb_32396.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbb_32396/03_2026/7wbb_32396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wbb_32396/03_2026/7wbb_32396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbb_32396/03_2026/7wbb_32396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wbb_32396/03_2026/7wbb_32396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbb_32396/03_2026/7wbb_32396.map" } resolution = 3.6 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 131 5.16 5 C 21146 2.51 5 N 5771 2.21 5 O 6553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33634 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5567 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 40, 'TRANS': 685} Chain breaks: 1 Chain: "B" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5567 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 40, 'TRANS': 685} Chain breaks: 1 Chain: "D" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5567 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 40, 'TRANS': 685} Chain breaks: 1 Chain: "E" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5567 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 40, 'TRANS': 685} Chain breaks: 1 Chain: "F" Number of atoms: 5348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5348 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 39, 'TRANS': 659} Chain breaks: 4 Chain: "H" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5567 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 40, 'TRANS': 685} Chain breaks: 1 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.33, per 1000 atoms: 0.22 Number of scatterers: 33634 At special positions: 0 Unit cell: (153.265, 160.664, 125.783, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 33 15.00 O 6553 8.00 N 5771 7.00 C 21146 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 seconds 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8058 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 28 sheets defined 48.1% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.738A pdb=" N LEU A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.644A pdb=" N TYR A 236 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 250 through 266 Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 268 through 272 removed outlier: 3.639A pdb=" N PHE A 271 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.667A pdb=" N LEU A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 338 removed outlier: 4.435A pdb=" N LEU A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.686A pdb=" N GLY A 360 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 361' Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.728A pdb=" N VAL A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.558A pdb=" N PHE A 405 " --> pdb=" O PRO A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 431 Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 453 through 477 Processing helix chain 'A' and resid 480 through 484 removed outlier: 4.194A pdb=" N SER A 483 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 499 removed outlier: 3.596A pdb=" N VAL A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ARG A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.641A pdb=" N LYS A 525 " --> pdb=" O GLN A 521 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Proline residue: A 535 - end of helix removed outlier: 4.399A pdb=" N ALA A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 Processing helix chain 'A' and resid 562 through 574 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.759A pdb=" N ALA A 620 " --> pdb=" O GLN A 617 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 621 " --> pdb=" O ILE A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 621' Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 661 through 665 removed outlier: 3.529A pdb=" N GLU A 664 " --> pdb=" O ARG A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 710 through 716 Processing helix chain 'A' and resid 720 through 740 removed outlier: 3.667A pdb=" N ASP A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.610A pdb=" N PHE A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 777 removed outlier: 3.673A pdb=" N LEU A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 99 through 107 removed outlier: 4.588A pdb=" N VAL B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.560A pdb=" N LEU B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.885A pdb=" N SER B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Proline residue: B 264 - end of helix Processing helix chain 'B' and resid 267 through 273 Processing helix chain 'B' and resid 291 through 303 removed outlier: 3.501A pdb=" N SER B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.812A pdb=" N ILE B 315 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 338 removed outlier: 4.392A pdb=" N LEU B 327 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 361 through 377 removed outlier: 3.776A pdb=" N MET B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.727A pdb=" N VAL B 395 " --> pdb=" O PRO B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.889A pdb=" N ASP B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 453 through 476 Processing helix chain 'B' and resid 480 through 484 Processing helix chain 'B' and resid 487 through 498 Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 521 through 538 removed outlier: 4.110A pdb=" N LYS B 525 " --> pdb=" O GLN B 521 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 538 through 546 removed outlier: 4.033A pdb=" N PHE B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 573 Processing helix chain 'B' and resid 583 through 587 removed outlier: 4.293A pdb=" N ILE B 586 " --> pdb=" O GLY B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 608 Processing helix chain 'B' and resid 618 through 621 removed outlier: 3.673A pdb=" N LEU B 621 " --> pdb=" O ILE B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 630 through 645 removed outlier: 3.806A pdb=" N ASN B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 665 Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.502A pdb=" N LEU B 670 " --> pdb=" O ASP B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 698 Processing helix chain 'B' and resid 701 through 706 Processing helix chain 'B' and resid 710 through 716 Processing helix chain 'B' and resid 720 through 740 removed outlier: 3.605A pdb=" N VAL B 725 " --> pdb=" O GLY B 721 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.569A pdb=" N PHE B 750 " --> pdb=" O GLU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 777 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.755A pdb=" N LEU D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.544A pdb=" N TYR D 236 " --> pdb=" O ASN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 Proline residue: D 264 - end of helix Processing helix chain 'D' and resid 291 through 303 Processing helix chain 'D' and resid 312 through 316 removed outlier: 4.362A pdb=" N ILE D 315 " --> pdb=" O GLY D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.550A pdb=" N LEU D 327 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 removed outlier: 3.730A pdb=" N ILE D 350 " --> pdb=" O GLN D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 375 Processing helix chain 'D' and resid 415 through 435 removed outlier: 3.691A pdb=" N MET D 430 " --> pdb=" O GLN D 426 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASP D 433 " --> pdb=" O ARG D 429 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 434 " --> pdb=" O MET D 430 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 449 Processing helix chain 'D' and resid 453 through 476 Processing helix chain 'D' and resid 480 through 484 Processing helix chain 'D' and resid 488 through 498 Processing helix chain 'D' and resid 501 through 506 removed outlier: 3.840A pdb=" N GLU D 505 " --> pdb=" O ALA D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 Processing helix chain 'D' and resid 521 through 538 removed outlier: 4.187A pdb=" N LEU D 534 " --> pdb=" O GLU D 530 " (cutoff:3.500A) Proline residue: D 535 - end of helix removed outlier: 3.792A pdb=" N ALA D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 546 removed outlier: 4.151A pdb=" N PHE D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 575 removed outlier: 4.535A pdb=" N GLY D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 587 removed outlier: 3.916A pdb=" N PHE D 587 " --> pdb=" O GLY D 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 583 through 587' Processing helix chain 'D' and resid 593 through 608 Processing helix chain 'D' and resid 618 through 621 Processing helix chain 'D' and resid 632 through 646 Processing helix chain 'D' and resid 666 through 671 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 701 through 706 Processing helix chain 'D' and resid 710 through 716 Processing helix chain 'D' and resid 720 through 740 Processing helix chain 'D' and resid 746 through 757 removed outlier: 3.819A pdb=" N ILE D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 774 removed outlier: 4.140A pdb=" N LEU D 766 " --> pdb=" O THR D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 61 Processing helix chain 'E' and resid 101 through 106 removed outlier: 4.104A pdb=" N GLY E 106 " --> pdb=" O ILE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.767A pdb=" N LYS E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 155 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.790A pdb=" N TYR E 236 " --> pdb=" O ASN E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 267 removed outlier: 3.751A pdb=" N SER E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Proline residue: E 264 - end of helix Processing helix chain 'E' and resid 267 through 275 removed outlier: 4.355A pdb=" N PHE E 271 " --> pdb=" O GLN E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 302 Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 322 through 337 removed outlier: 3.746A pdb=" N TYR E 337 " --> pdb=" O GLU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 removed outlier: 3.518A pdb=" N ILE E 350 " --> pdb=" O GLN E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 375 Processing helix chain 'E' and resid 415 through 430 removed outlier: 4.199A pdb=" N MET E 430 " --> pdb=" O GLN E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 449 removed outlier: 3.560A pdb=" N ILE E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 473 removed outlier: 3.775A pdb=" N THR E 458 " --> pdb=" O GLY E 454 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 473 " --> pdb=" O ILE E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 495 removed outlier: 3.766A pdb=" N VAL E 491 " --> pdb=" O THR E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 538 removed outlier: 3.791A pdb=" N LYS E 525 " --> pdb=" O GLN E 521 " (cutoff:3.500A) Proline residue: E 535 - end of helix Processing helix chain 'E' and resid 538 through 546 removed outlier: 3.787A pdb=" N PHE E 542 " --> pdb=" O ALA E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 575 removed outlier: 3.791A pdb=" N LEU E 570 " --> pdb=" O THR E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 587 removed outlier: 4.116A pdb=" N ILE E 586 " --> pdb=" O LYS E 582 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE E 587 " --> pdb=" O GLY E 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 582 through 587' Processing helix chain 'E' and resid 592 through 608 Processing helix chain 'E' and resid 617 through 621 removed outlier: 3.560A pdb=" N LEU E 621 " --> pdb=" O ILE E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 645 removed outlier: 3.512A pdb=" N ASN E 634 " --> pdb=" O THR E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 665 removed outlier: 3.938A pdb=" N GLU E 664 " --> pdb=" O ARG E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 666 through 671 Processing helix chain 'E' and resid 685 through 700 removed outlier: 4.235A pdb=" N LYS E 699 " --> pdb=" O LYS E 695 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE E 700 " --> pdb=" O CYS E 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 706 Processing helix chain 'E' and resid 709 through 718 Processing helix chain 'E' and resid 720 through 739 removed outlier: 3.616A pdb=" N VAL E 724 " --> pdb=" O SER E 720 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 725 " --> pdb=" O GLY E 721 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 757 removed outlier: 4.023A pdb=" N PHE E 750 " --> pdb=" O GLU E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 775 removed outlier: 4.063A pdb=" N LEU E 766 " --> pdb=" O THR E 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 61 Processing helix chain 'F' and resid 99 through 106 removed outlier: 3.535A pdb=" N VAL F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.549A pdb=" N LEU F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 267 Proline residue: F 264 - end of helix removed outlier: 3.818A pdb=" N GLN F 267 " --> pdb=" O ILE F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 275 removed outlier: 4.017A pdb=" N PHE F 271 " --> pdb=" O GLN F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 302 Processing helix chain 'F' and resid 322 through 337 removed outlier: 3.891A pdb=" N TYR F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 360 through 377 Processing helix chain 'F' and resid 415 through 430 Processing helix chain 'F' and resid 438 through 449 Processing helix chain 'F' and resid 456 through 477 removed outlier: 3.745A pdb=" N LEU F 460 " --> pdb=" O ASP F 456 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS F 461 " --> pdb=" O LEU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 484 Processing helix chain 'F' and resid 488 through 499 Processing helix chain 'F' and resid 521 through 538 removed outlier: 4.001A pdb=" N THR F 526 " --> pdb=" O GLU F 522 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS F 527 " --> pdb=" O GLU F 523 " (cutoff:3.500A) Proline residue: F 535 - end of helix removed outlier: 3.594A pdb=" N ALA F 538 " --> pdb=" O LEU F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 546 Processing helix chain 'F' and resid 562 through 575 Processing helix chain 'F' and resid 600 through 609 removed outlier: 3.707A pdb=" N ALA F 605 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG F 606 " --> pdb=" O PHE F 602 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 651 removed outlier: 4.447A pdb=" N ASN F 642 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU F 643 " --> pdb=" O SER F 639 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU F 650 " --> pdb=" O GLY F 646 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS F 651 " --> pdb=" O VAL F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 661 through 665 Processing helix chain 'F' and resid 666 through 671 removed outlier: 3.726A pdb=" N ARG F 671 " --> pdb=" O ALA F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 699 removed outlier: 4.251A pdb=" N LYS F 699 " --> pdb=" O LYS F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 710 through 716 Processing helix chain 'F' and resid 722 through 739 removed outlier: 4.010A pdb=" N LEU F 726 " --> pdb=" O ALA F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 757 removed outlier: 3.909A pdb=" N PHE F 750 " --> pdb=" O GLU F 746 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 757 " --> pdb=" O ALA F 753 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 777 removed outlier: 3.836A pdb=" N LEU F 766 " --> pdb=" O THR F 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 61 Processing helix chain 'C' and resid 99 through 106 removed outlier: 3.559A pdb=" N GLY C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.653A pdb=" N GLN C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.857A pdb=" N TYR C 236 " --> pdb=" O ASN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.513A pdb=" N VAL C 247 " --> pdb=" O TYR C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 266 Proline residue: C 264 - end of helix Processing helix chain 'C' and resid 268 through 275 Processing helix chain 'C' and resid 291 through 303 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.915A pdb=" N ILE C 315 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 removed outlier: 4.199A pdb=" N LEU C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 337 " --> pdb=" O GLU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 removed outlier: 3.871A pdb=" N ILE C 350 " --> pdb=" O GLN C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 375 Processing helix chain 'C' and resid 391 through 395 Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.834A pdb=" N ASP C 406 " --> pdb=" O PRO C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 430 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 453 through 476 Processing helix chain 'C' and resid 480 through 484 removed outlier: 3.622A pdb=" N SER C 483 " --> pdb=" O ASP C 480 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 484 " --> pdb=" O LYS C 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 480 through 484' Processing helix chain 'C' and resid 487 through 498 Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.585A pdb=" N ILE C 518 " --> pdb=" O TRP C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 538 removed outlier: 4.325A pdb=" N LYS C 525 " --> pdb=" O GLN C 521 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C 534 " --> pdb=" O GLU C 530 " (cutoff:3.500A) Proline residue: C 535 - end of helix Processing helix chain 'C' and resid 538 through 546 removed outlier: 4.320A pdb=" N PHE C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 574 Processing helix chain 'C' and resid 592 through 608 Processing helix chain 'C' and resid 617 through 622 removed outlier: 4.249A pdb=" N LEU C 621 " --> pdb=" O GLN C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 646 Processing helix chain 'C' and resid 685 through 698 Processing helix chain 'C' and resid 701 through 706 removed outlier: 3.642A pdb=" N SER C 705 " --> pdb=" O ASN C 701 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY C 706 " --> pdb=" O THR C 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 701 through 706' Processing helix chain 'C' and resid 710 through 716 Processing helix chain 'C' and resid 720 through 740 removed outlier: 3.548A pdb=" N VAL C 724 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 725 " --> pdb=" O GLY C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.807A pdb=" N PHE C 750 " --> pdb=" O GLU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 777 removed outlier: 3.969A pdb=" N LEU C 766 " --> pdb=" O THR C 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.688A pdb=" N ALA A 51 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 71 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A 70 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 117 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 72 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 183 removed outlier: 7.356A pdb=" N THR A 130 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A 129 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 removed outlier: 6.710A pdb=" N LEU A 284 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 342 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA A 388 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE A 344 " --> pdb=" O ALA A 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 579 through 581 removed outlier: 3.840A pdb=" N PHE A 614 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 581 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 613 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA A 658 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE A 615 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY A 552 " --> pdb=" O ARG A 677 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE A 679 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 554 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.365A pdb=" N ILE B 35 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU B 98 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ARG B 37 " --> pdb=" O LEU B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 72 removed outlier: 4.166A pdb=" N THR B 70 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 117 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 72 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 178 through 179 removed outlier: 3.688A pdb=" N LYS B 128 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.919A pdb=" N VAL B 129 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER B 227 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL B 131 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 306 through 309 removed outlier: 6.168A pdb=" N HIS B 306 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE B 343 " --> pdb=" O HIS B 306 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 308 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ASP B 345 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER B 340 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE B 386 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B 342 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA B 388 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 344 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 281 " --> pdb=" O GLN B 407 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL B 409 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 283 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 578 through 581 removed outlier: 6.935A pdb=" N LEU B 579 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP B 616 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 581 " --> pdb=" O ASP B 616 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE B 613 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ALA B 658 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE B 615 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY B 552 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE B 679 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU B 554 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.512A pdb=" N GLY D 72 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE D 35 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 163 through 164 removed outlier: 3.775A pdb=" N PHE D 164 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D 178 " --> pdb=" O PHE D 164 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR D 130 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA D 183 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS D 128 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 157 through 158 Processing sheet with id=AB6, first strand: chain 'D' and resid 306 through 309 removed outlier: 6.190A pdb=" N HIS D 306 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE D 343 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU D 308 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASP D 345 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N SER D 340 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE D 386 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE D 342 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA D 388 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 344 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU D 283 " --> pdb=" O VAL D 409 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 578 through 582 removed outlier: 6.544A pdb=" N LEU D 579 " --> pdb=" O PHE D 614 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASP D 616 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL D 581 " --> pdb=" O ASP D 616 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE D 613 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA D 658 " --> pdb=" O ILE D 613 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE D 615 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL D 553 " --> pdb=" O ALA D 657 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N THR D 659 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU D 555 " --> pdb=" O THR D 659 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY D 552 " --> pdb=" O ARG D 677 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE D 679 " --> pdb=" O GLY D 552 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU D 554 " --> pdb=" O ILE D 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 34 through 38 removed outlier: 5.936A pdb=" N ILE E 35 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU E 98 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ARG E 37 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR E 97 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR E 52 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA E 51 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE E 34 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 180 through 183 removed outlier: 3.853A pdb=" N ASP E 182 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 307 through 311 removed outlier: 6.025A pdb=" N LEU E 308 " --> pdb=" O PHE E 343 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP E 345 " --> pdb=" O LEU E 308 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE E 310 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY E 281 " --> pdb=" O GLN E 407 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL E 409 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU E 283 " --> pdb=" O VAL E 409 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 578 through 581 removed outlier: 6.207A pdb=" N LEU E 579 " --> pdb=" O PHE E 614 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE E 613 " --> pdb=" O VAL E 656 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA E 658 " --> pdb=" O ILE E 613 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE E 615 " --> pdb=" O ALA E 658 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL E 553 " --> pdb=" O ALA E 657 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 659 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU E 555 " --> pdb=" O THR E 659 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR E 556 " --> pdb=" O ILE E 679 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 35 through 37 removed outlier: 5.988A pdb=" N ILE F 35 " --> pdb=" O ILE F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 50 through 52 removed outlier: 6.249A pdb=" N ALA F 51 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR F 70 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS F 117 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY F 72 " --> pdb=" O GLU F 115 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 178 through 182 removed outlier: 3.663A pdb=" N THR F 181 " --> pdb=" O THR F 130 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR F 130 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER F 133 " --> pdb=" O SER F 227 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 306 through 310 removed outlier: 6.162A pdb=" N HIS F 306 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE F 343 " --> pdb=" O HIS F 306 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU F 308 " --> pdb=" O PHE F 343 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP F 345 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE F 310 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER F 340 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE F 386 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE F 342 " --> pdb=" O ILE F 386 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA F 388 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE F 344 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE F 282 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL F 409 " --> pdb=" O GLY F 281 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU F 283 " --> pdb=" O VAL F 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 614 through 615 removed outlier: 6.601A pdb=" N PHE F 615 " --> pdb=" O ALA F 658 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL F 553 " --> pdb=" O ALA F 657 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR F 659 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU F 555 " --> pdb=" O THR F 659 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU F 554 " --> pdb=" O ILE F 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 78 through 80 removed outlier: 3.854A pdb=" N THR C 70 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 117 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE C 35 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.395A pdb=" N HIS C 306 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE C 343 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 308 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASP C 345 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ILE C 310 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER C 340 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE C 386 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE C 342 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA C 388 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 344 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY C 281 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL C 409 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU C 283 " --> pdb=" O VAL C 409 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 578 through 582 removed outlier: 6.749A pdb=" N LEU C 579 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASP C 616 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL C 581 " --> pdb=" O ASP C 616 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL C 553 " --> pdb=" O ALA C 657 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR C 659 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU C 555 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 556 " --> pdb=" O ILE C 679 " (cutoff:3.500A) 1287 hydrogen bonds defined for protein. 3678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5748 1.31 - 1.43: 8077 1.43 - 1.56: 20129 1.56 - 1.69: 55 1.69 - 1.82: 220 Bond restraints: 34229 Sorted by residual: bond pdb=" C PRO A 264 " pdb=" O PRO A 264 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" N LYS B 563 " pdb=" CA LYS B 563 " ideal model delta sigma weight residual 1.459 1.498 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ILE A 261 " pdb=" CA ILE A 261 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N GLY A 248 " pdb=" CA GLY A 248 " ideal model delta sigma weight residual 1.444 1.475 -0.032 1.02e-02 9.61e+03 9.55e+00 bond pdb=" N SER B 562 " pdb=" CA SER B 562 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.32e+00 ... (remaining 34224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 45673 2.04 - 4.08: 647 4.08 - 6.12: 77 6.12 - 8.17: 11 8.17 - 10.21: 7 Bond angle restraints: 46415 Sorted by residual: angle pdb=" C LYS B 563 " pdb=" N THR B 564 " pdb=" CA THR B 564 " ideal model delta sigma weight residual 120.29 129.36 -9.07 1.42e+00 4.96e-01 4.08e+01 angle pdb=" C SER E 432 " pdb=" N ASP E 433 " pdb=" CA ASP E 433 " ideal model delta sigma weight residual 123.91 134.12 -10.21 1.66e+00 3.63e-01 3.78e+01 angle pdb=" C ILE A 261 " pdb=" N GLU A 262 " pdb=" CA GLU A 262 " ideal model delta sigma weight residual 120.29 128.54 -8.25 1.42e+00 4.96e-01 3.37e+01 angle pdb=" O ILE A 261 " pdb=" C ILE A 261 " pdb=" N GLU A 262 " ideal model delta sigma weight residual 121.83 127.22 -5.39 1.03e+00 9.43e-01 2.74e+01 angle pdb=" N LYS B 563 " pdb=" CA LYS B 563 " pdb=" C LYS B 563 " ideal model delta sigma weight residual 111.07 116.32 -5.25 1.07e+00 8.73e-01 2.41e+01 ... (remaining 46410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 18833 17.86 - 35.71: 1875 35.71 - 53.57: 430 53.57 - 71.42: 51 71.42 - 89.28: 18 Dihedral angle restraints: 21207 sinusoidal: 8714 harmonic: 12493 Sorted by residual: dihedral pdb=" C LYS E 563 " pdb=" N LYS E 563 " pdb=" CA LYS E 563 " pdb=" CB LYS E 563 " ideal model delta harmonic sigma weight residual -122.60 -133.85 11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CA SER E 99 " pdb=" C SER E 99 " pdb=" N THR E 100 " pdb=" CA THR E 100 " ideal model delta harmonic sigma weight residual 180.00 158.69 21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" N LYS E 563 " pdb=" C LYS E 563 " pdb=" CA LYS E 563 " pdb=" CB LYS E 563 " ideal model delta harmonic sigma weight residual 122.80 132.13 -9.33 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 21204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4755 0.068 - 0.136: 588 0.136 - 0.205: 21 0.205 - 0.273: 4 0.273 - 0.341: 2 Chirality restraints: 5370 Sorted by residual: chirality pdb=" CA LYS E 563 " pdb=" N LYS E 563 " pdb=" C LYS E 563 " pdb=" CB LYS E 563 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA THR E 564 " pdb=" N THR E 564 " pdb=" C THR E 564 " pdb=" CB THR E 564 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CB ILE C 310 " pdb=" CA ILE C 310 " pdb=" CG1 ILE C 310 " pdb=" CG2 ILE C 310 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 5367 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 609 " 0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 610 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 261 " -0.013 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C ILE A 261 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 261 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 262 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 432 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C SER E 432 " -0.047 2.00e-02 2.50e+03 pdb=" O SER E 432 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E 433 " 0.015 2.00e-02 2.50e+03 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3177 2.75 - 3.28: 34205 3.28 - 3.82: 55315 3.82 - 4.36: 60892 4.36 - 4.90: 105370 Nonbonded interactions: 258959 Sorted by model distance: nonbonded pdb=" OD1 ASP C 456 " pdb=" OG SER C 501 " model vdw 2.206 3.040 nonbonded pdb=" O ASN E 660 " pdb=" OH TYR E 769 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 720 " pdb=" OE1 GLU A 723 " model vdw 2.229 3.040 nonbonded pdb=" O ASN E 577 " pdb=" OG SER E 611 " model vdw 2.233 3.040 nonbonded pdb=" O ALA E 334 " pdb=" OG SER E 340 " model vdw 2.239 3.040 ... (remaining 258954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 801)) selection = (chain 'B' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 801)) selection = (chain 'C' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 801)) selection = (chain 'D' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 801)) selection = (chain 'E' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 801)) selection = chain 'F' } 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.560 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.002 0.056 34229 Z= 0.141 Angle : 0.551 10.207 46415 Z= 0.302 Chirality : 0.043 0.341 5370 Planarity : 0.004 0.088 5976 Dihedral : 14.717 89.278 13149 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.05 % Favored : 94.60 % Rotamer: Outliers : 0.11 % Allowed : 0.49 % Favored : 99.40 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.91 (0.13), residues: 4299 helix: 1.99 (0.13), residues: 1732 sheet: 0.58 (0.27), residues: 426 loop : -0.55 (0.14), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 328 TYR 0.012 0.000 TYR A 337 PHE 0.017 0.001 PHE B 274 TRP 0.003 0.000 TRP D 515 HIS 0.007 0.000 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00228 (34229) covalent geometry : angle 0.55069 (46415) hydrogen bonds : bond 0.15291 ( 1285) hydrogen bonds : angle 5.67206 ( 3678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 327 time to evaluate : 1.275 Fit side-chains REVERT: B 374 MET cc_start: 0.8744 (tpp) cc_final: 0.8539 (tpp) REVERT: E 109 ILE cc_start: 0.8793 (mt) cc_final: 0.8303 (tt) REVERT: E 507 PHE cc_start: 0.3057 (t80) cc_final: 0.2852 (t80) REVERT: E 755 LYS cc_start: 0.6469 (ptmt) cc_final: 0.5691 (mmtm) outliers start: 4 outliers final: 1 residues processed: 330 average time/residue: 0.1749 time to fit residues: 101.4390 Evaluate side-chains 239 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0470 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS D 407 GLN ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN D 729 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 HIS C 231 GLN C 729 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.139004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100937 restraints weight = 74719.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.100291 restraints weight = 62079.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100183 restraints weight = 49489.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.100556 restraints weight = 42786.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.100700 restraints weight = 38519.459| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34229 Z= 0.174 Angle : 0.593 9.685 46415 Z= 0.301 Chirality : 0.044 0.217 5370 Planarity : 0.004 0.055 5976 Dihedral : 9.243 85.678 5037 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.49 % Favored : 94.16 % Rotamer: Outliers : 1.02 % Allowed : 7.19 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.72 (0.13), residues: 4299 helix: 1.73 (0.13), residues: 1750 sheet: 0.41 (0.25), residues: 467 loop : -0.58 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 434 TYR 0.019 0.001 TYR B 337 PHE 0.018 0.001 PHE B 271 TRP 0.009 0.001 TRP C 515 HIS 0.013 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00406 (34229) covalent geometry : angle 0.59335 (46415) hydrogen bonds : bond 0.03462 ( 1285) hydrogen bonds : angle 4.26980 ( 3678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6878 (pp20) REVERT: A 765 MET cc_start: 0.7910 (ptt) cc_final: 0.7622 (ptp) REVERT: E 162 MET cc_start: 0.8089 (mmt) cc_final: 0.7745 (mmt) REVERT: F 159 MET cc_start: 0.4180 (mmm) cc_final: 0.3795 (mmm) REVERT: F 261 ILE cc_start: 0.8625 (pt) cc_final: 0.8414 (mt) outliers start: 37 outliers final: 28 residues processed: 272 average time/residue: 0.1871 time to fit residues: 88.2861 Evaluate side-chains 241 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 88 optimal weight: 9.9990 chunk 377 optimal weight: 0.0370 chunk 379 optimal weight: 6.9990 chunk 351 optimal weight: 20.0000 chunk 274 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 239 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 overall best weight: 5.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 304 ASN B 149 GLN B 390 ASN D 91 HIS E 107 ASN E 301 ASN F 149 GLN F 166 ASN C 77 ASN C 138 ASN C 450 HIS ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.130973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092355 restraints weight = 74146.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088909 restraints weight = 78424.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089668 restraints weight = 58695.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.090915 restraints weight = 45792.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090745 restraints weight = 39614.111| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 34229 Z= 0.306 Angle : 0.730 10.910 46415 Z= 0.373 Chirality : 0.049 0.270 5370 Planarity : 0.006 0.067 5976 Dihedral : 9.695 88.654 5037 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.30 % Favored : 93.32 % Rotamer: Outliers : 2.50 % Allowed : 10.79 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.09 (0.13), residues: 4299 helix: 1.15 (0.12), residues: 1764 sheet: 0.25 (0.25), residues: 482 loop : -0.95 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 419 TYR 0.065 0.002 TYR C 210 PHE 0.025 0.002 PHE C 209 TRP 0.020 0.002 TRP C 515 HIS 0.014 0.002 HIS C 450 Details of bonding type rmsd covalent geometry : bond 0.00727 (34229) covalent geometry : angle 0.73046 (46415) hydrogen bonds : bond 0.04546 ( 1285) hydrogen bonds : angle 4.68490 ( 3678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 203 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8759 (tt) REVERT: A 430 MET cc_start: 0.8264 (ppp) cc_final: 0.7612 (ppp) REVERT: A 643 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: B 42 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7725 (mtmt) REVERT: B 74 ILE cc_start: 0.8776 (mm) cc_final: 0.8360 (mm) REVERT: E 503 MET cc_start: 0.6746 (tpt) cc_final: 0.6392 (tpt) REVERT: C 294 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8291 (ttm) REVERT: C 309 THR cc_start: 0.8815 (m) cc_final: 0.8387 (p) outliers start: 91 outliers final: 61 residues processed: 280 average time/residue: 0.1750 time to fit residues: 86.4134 Evaluate side-chains 248 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 184 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 159 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 380 optimal weight: 0.0070 chunk 18 optimal weight: 30.0000 chunk 340 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 HIS ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.132229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091740 restraints weight = 73508.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089943 restraints weight = 57606.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090676 restraints weight = 43000.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090985 restraints weight = 38440.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.090859 restraints weight = 34935.361| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34229 Z= 0.178 Angle : 0.592 9.489 46415 Z= 0.301 Chirality : 0.044 0.172 5370 Planarity : 0.004 0.064 5976 Dihedral : 9.312 86.868 5037 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.79 % Favored : 93.79 % Rotamer: Outliers : 2.20 % Allowed : 13.70 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.26 (0.13), residues: 4299 helix: 1.41 (0.13), residues: 1753 sheet: 0.17 (0.24), residues: 476 loop : -0.91 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 689 TYR 0.016 0.001 TYR C 210 PHE 0.019 0.001 PHE E 754 TRP 0.005 0.001 TRP B 515 HIS 0.008 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00421 (34229) covalent geometry : angle 0.59248 (46415) hydrogen bonds : bond 0.03462 ( 1285) hydrogen bonds : angle 4.36616 ( 3678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 202 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.8285 (ppp) cc_final: 0.7527 (ppp) REVERT: B 42 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7811 (mtmt) REVERT: B 74 ILE cc_start: 0.8762 (mm) cc_final: 0.8349 (mm) REVERT: D 80 LEU cc_start: 0.8495 (mp) cc_final: 0.8204 (mt) REVERT: D 377 MET cc_start: 0.8294 (mmm) cc_final: 0.8070 (mmm) REVERT: E 473 LEU cc_start: 0.8089 (tp) cc_final: 0.7878 (mp) REVERT: E 664 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6138 (pm20) REVERT: C 294 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8078 (ttm) outliers start: 80 outliers final: 56 residues processed: 268 average time/residue: 0.1796 time to fit residues: 84.6892 Evaluate side-chains 240 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 182 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 117 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 310 optimal weight: 2.9990 chunk 393 optimal weight: 0.9990 chunk 269 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 380 optimal weight: 0.3980 chunk 31 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.131780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094753 restraints weight = 74083.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.091303 restraints weight = 73090.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.092207 restraints weight = 67288.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.092266 restraints weight = 49105.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092444 restraints weight = 43706.826| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34229 Z= 0.176 Angle : 0.588 8.682 46415 Z= 0.298 Chirality : 0.044 0.172 5370 Planarity : 0.004 0.062 5976 Dihedral : 9.140 87.413 5037 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.26 % Favored : 93.30 % Rotamer: Outliers : 2.77 % Allowed : 14.28 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.23 (0.13), residues: 4299 helix: 1.41 (0.13), residues: 1770 sheet: -0.03 (0.24), residues: 474 loop : -0.91 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 759 TYR 0.021 0.001 TYR C 210 PHE 0.016 0.001 PHE E 754 TRP 0.004 0.001 TRP B 515 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00418 (34229) covalent geometry : angle 0.58792 (46415) hydrogen bonds : bond 0.03403 ( 1285) hydrogen bonds : angle 4.31500 ( 3678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 198 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.8237 (ppp) cc_final: 0.7412 (ppp) REVERT: B 42 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7809 (mtmt) REVERT: B 74 ILE cc_start: 0.8734 (mm) cc_final: 0.8294 (mm) REVERT: B 595 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7801 (mp0) REVERT: D 377 MET cc_start: 0.8315 (mmm) cc_final: 0.8109 (mmm) REVERT: E 430 MET cc_start: 0.6267 (tmm) cc_final: 0.5612 (mtm) REVERT: E 473 LEU cc_start: 0.8035 (tp) cc_final: 0.7827 (mp) REVERT: E 664 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6208 (pm20) REVERT: F 137 TYR cc_start: 0.4791 (m-10) cc_final: 0.4449 (m-10) REVERT: F 143 MET cc_start: 0.4724 (OUTLIER) cc_final: 0.4206 (ppp) REVERT: F 263 ILE cc_start: 0.8140 (mt) cc_final: 0.7903 (mt) outliers start: 101 outliers final: 72 residues processed: 281 average time/residue: 0.1808 time to fit residues: 89.2784 Evaluate side-chains 256 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 182 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 307 optimal weight: 0.0670 chunk 63 optimal weight: 0.0370 chunk 104 optimal weight: 9.9990 chunk 385 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 369 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.132229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093508 restraints weight = 73036.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091559 restraints weight = 57902.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092107 restraints weight = 45604.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092430 restraints weight = 39294.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092396 restraints weight = 35787.669| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34229 Z= 0.127 Angle : 0.562 9.490 46415 Z= 0.284 Chirality : 0.043 0.173 5370 Planarity : 0.004 0.059 5976 Dihedral : 8.959 82.537 5037 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.86 % Favored : 93.72 % Rotamer: Outliers : 2.39 % Allowed : 15.46 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.34 (0.13), residues: 4299 helix: 1.54 (0.13), residues: 1766 sheet: -0.07 (0.24), residues: 479 loop : -0.87 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 689 TYR 0.019 0.001 TYR D 680 PHE 0.016 0.001 PHE C 209 TRP 0.006 0.001 TRP A 515 HIS 0.007 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00295 (34229) covalent geometry : angle 0.56247 (46415) hydrogen bonds : bond 0.03073 ( 1285) hydrogen bonds : angle 4.20161 ( 3678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 197 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.3593 (pt) cc_final: 0.2724 (tp) REVERT: A 430 MET cc_start: 0.8162 (ppp) cc_final: 0.7390 (ppp) REVERT: A 643 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: B 42 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7830 (mtmt) REVERT: B 74 ILE cc_start: 0.8787 (mm) cc_final: 0.8375 (mm) REVERT: D 377 MET cc_start: 0.8335 (mmm) cc_final: 0.8116 (mmm) REVERT: E 473 LEU cc_start: 0.8244 (tp) cc_final: 0.7876 (mp) REVERT: F 137 TYR cc_start: 0.4885 (m-10) cc_final: 0.4648 (m-10) REVERT: F 143 MET cc_start: 0.4786 (OUTLIER) cc_final: 0.4284 (ppp) REVERT: F 263 ILE cc_start: 0.8194 (mt) cc_final: 0.7949 (mt) REVERT: C 53 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8475 (mt) outliers start: 87 outliers final: 62 residues processed: 270 average time/residue: 0.1799 time to fit residues: 85.2307 Evaluate side-chains 248 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 183 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 197 optimal weight: 4.9990 chunk 15 optimal weight: 40.0000 chunk 224 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 297 optimal weight: 30.0000 chunk 295 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 341 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 338 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 122 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** C 642 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 = 0.3934 r_free = 0.3934 target = 0.127704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.090162 restraints weight = 74120.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086731 restraints weight = 71516.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.087583 restraints weight = 64320.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087701 restraints weight = 44910.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.088452 restraints weight = 42930.576| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.112 34229 Z= 0.391 Angle : 0.773 10.754 46415 Z= 0.393 Chirality : 0.050 0.278 5370 Planarity : 0.006 0.073 5976 Dihedral : 9.289 82.274 5037 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.07 % Favored : 92.51 % Rotamer: Outliers : 3.10 % Allowed : 15.87 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.24 (0.13), residues: 4299 helix: 0.98 (0.12), residues: 1777 sheet: -0.33 (0.24), residues: 471 loop : -1.14 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 689 TYR 0.031 0.002 TYR D 768 PHE 0.020 0.002 PHE B 34 TRP 0.007 0.001 TRP B 515 HIS 0.008 0.002 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00926 (34229) covalent geometry : angle 0.77305 (46415) hydrogen bonds : bond 0.04481 ( 1285) hydrogen bonds : angle 4.72895 ( 3678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 185 time to evaluate : 1.371 Fit side-chains REVERT: A 140 LEU cc_start: 0.4036 (pt) cc_final: 0.2817 (tp) REVERT: A 406 ASP cc_start: 0.6850 (m-30) cc_final: 0.6613 (t0) REVERT: A 430 MET cc_start: 0.8327 (ppp) cc_final: 0.7436 (ppp) REVERT: B 42 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7732 (mtmt) REVERT: B 74 ILE cc_start: 0.8919 (mm) cc_final: 0.8552 (mm) REVERT: D 143 MET cc_start: 0.6943 (mpp) cc_final: 0.5571 (tpt) REVERT: D 215 PHE cc_start: 0.8048 (m-80) cc_final: 0.7765 (m-80) REVERT: E 430 MET cc_start: 0.6846 (tmm) cc_final: 0.6161 (mtm) REVERT: E 664 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.6795 (pm20) REVERT: F 263 ILE cc_start: 0.8227 (mt) cc_final: 0.7998 (mt) REVERT: C 53 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8638 (mt) REVERT: C 253 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7490 (mt-10) outliers start: 113 outliers final: 84 residues processed: 285 average time/residue: 0.1793 time to fit residues: 91.1357 Evaluate side-chains 265 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 178 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 347 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 270 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 250 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 408 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.131544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.091972 restraints weight = 73597.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.090263 restraints weight = 54241.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.090722 restraints weight = 42160.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090959 restraints weight = 35948.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091044 restraints weight = 32904.350| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34229 Z= 0.116 Angle : 0.598 13.966 46415 Z= 0.299 Chirality : 0.043 0.325 5370 Planarity : 0.005 0.065 5976 Dihedral : 8.902 84.330 5037 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.77 % Favored : 93.86 % Rotamer: Outliers : 2.14 % Allowed : 16.94 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.10 (0.13), residues: 4299 helix: 1.35 (0.13), residues: 1776 sheet: -0.30 (0.24), residues: 476 loop : -0.99 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 689 TYR 0.023 0.001 TYR D 680 PHE 0.025 0.001 PHE B 34 TRP 0.011 0.001 TRP A 515 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00259 (34229) covalent geometry : angle 0.59846 (46415) hydrogen bonds : bond 0.03200 ( 1285) hydrogen bonds : angle 4.33162 ( 3678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 187 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.3901 (pt) cc_final: 0.2819 (tp) REVERT: A 430 MET cc_start: 0.8263 (ppp) cc_final: 0.7410 (ppp) REVERT: B 42 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7790 (mtmt) REVERT: B 74 ILE cc_start: 0.8809 (mm) cc_final: 0.8426 (mm) REVERT: B 528 MET cc_start: 0.8460 (mmm) cc_final: 0.8137 (mmm) REVERT: B 589 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8219 (ttpp) REVERT: D 143 MET cc_start: 0.6899 (mpp) cc_final: 0.5520 (tpt) REVERT: E 430 MET cc_start: 0.6641 (tmm) cc_final: 0.6019 (mtm) REVERT: E 664 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6210 (pm20) REVERT: F 143 MET cc_start: 0.5260 (OUTLIER) cc_final: 0.4872 (ppp) REVERT: F 263 ILE cc_start: 0.8168 (mt) cc_final: 0.7946 (mt) REVERT: F 374 MET cc_start: 0.5949 (ttp) cc_final: 0.5742 (tmm) REVERT: C 53 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8561 (mt) REVERT: C 595 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7570 (mp0) outliers start: 78 outliers final: 59 residues processed: 256 average time/residue: 0.1850 time to fit residues: 83.3282 Evaluate side-chains 241 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 366 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 392 optimal weight: 1.9990 chunk 271 optimal weight: 10.0000 chunk 316 optimal weight: 0.0470 chunk 389 optimal weight: 8.9990 chunk 11 optimal weight: 0.0570 chunk 283 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 402 optimal weight: 0.5980 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.131169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.091809 restraints weight = 73486.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091000 restraints weight = 51567.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.091544 restraints weight = 40562.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091696 restraints weight = 33818.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091695 restraints weight = 32545.335| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34229 Z= 0.137 Angle : 0.593 12.468 46415 Z= 0.297 Chirality : 0.044 0.363 5370 Planarity : 0.004 0.063 5976 Dihedral : 8.736 85.000 5037 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.28 % Favored : 93.32 % Rotamer: Outliers : 2.25 % Allowed : 16.75 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.15 (0.13), residues: 4299 helix: 1.40 (0.13), residues: 1777 sheet: -0.30 (0.24), residues: 483 loop : -0.96 (0.14), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 689 TYR 0.022 0.001 TYR D 680 PHE 0.025 0.001 PHE B 34 TRP 0.008 0.001 TRP A 515 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00321 (34229) covalent geometry : angle 0.59281 (46415) hydrogen bonds : bond 0.03226 ( 1285) hydrogen bonds : angle 4.25840 ( 3678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 183 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.3824 (pt) cc_final: 0.2772 (tp) REVERT: A 430 MET cc_start: 0.8222 (ppp) cc_final: 0.7372 (ppp) REVERT: B 42 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7770 (mtmt) REVERT: B 74 ILE cc_start: 0.8797 (mm) cc_final: 0.8404 (mm) REVERT: B 528 MET cc_start: 0.8532 (mmm) cc_final: 0.8175 (mmm) REVERT: B 589 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8225 (ttpp) REVERT: D 162 MET cc_start: 0.7971 (mtp) cc_final: 0.7624 (mtp) REVERT: D 528 MET cc_start: 0.8696 (mmm) cc_final: 0.8351 (mmm) REVERT: E 294 MET cc_start: 0.8168 (tpt) cc_final: 0.7952 (tpp) REVERT: E 430 MET cc_start: 0.6525 (tmm) cc_final: 0.6019 (mtp) REVERT: E 664 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6132 (pm20) REVERT: F 143 MET cc_start: 0.5274 (OUTLIER) cc_final: 0.4867 (ppp) REVERT: F 221 SER cc_start: 0.2813 (OUTLIER) cc_final: 0.2321 (m) REVERT: F 263 ILE cc_start: 0.8147 (mt) cc_final: 0.7929 (mt) REVERT: F 374 MET cc_start: 0.5978 (ttp) cc_final: 0.5752 (tmm) REVERT: F 765 MET cc_start: 0.1685 (ttt) cc_final: 0.1207 (ttt) REVERT: C 53 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8571 (mt) REVERT: C 595 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7609 (mp0) outliers start: 82 outliers final: 65 residues processed: 257 average time/residue: 0.1835 time to fit residues: 83.6371 Evaluate side-chains 248 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 177 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 203 optimal weight: 0.4980 chunk 356 optimal weight: 20.0000 chunk 4 optimal weight: 0.2980 chunk 347 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 228 optimal weight: 30.0000 chunk 317 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.131993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094435 restraints weight = 73985.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.090780 restraints weight = 71075.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091332 restraints weight = 55634.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091990 restraints weight = 43549.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.092124 restraints weight = 38762.741| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34229 Z= 0.117 Angle : 0.582 12.569 46415 Z= 0.290 Chirality : 0.044 0.367 5370 Planarity : 0.004 0.062 5976 Dihedral : 8.525 89.800 5037 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.91 % Favored : 93.70 % Rotamer: Outliers : 1.87 % Allowed : 17.30 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.22 (0.13), residues: 4299 helix: 1.45 (0.13), residues: 1777 sheet: -0.33 (0.24), residues: 460 loop : -0.90 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 689 TYR 0.021 0.001 TYR D 680 PHE 0.027 0.001 PHE B 34 TRP 0.008 0.001 TRP A 515 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00268 (34229) covalent geometry : angle 0.58202 (46415) hydrogen bonds : bond 0.02992 ( 1285) hydrogen bonds : angle 4.18512 ( 3678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 1.362 Fit side-chains REVERT: A 140 LEU cc_start: 0.4005 (pt) cc_final: 0.2960 (tp) REVERT: A 377 MET cc_start: 0.5633 (ttm) cc_final: 0.4263 (tmm) REVERT: A 430 MET cc_start: 0.8205 (ppp) cc_final: 0.7357 (ppp) REVERT: B 42 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7775 (mtmt) REVERT: B 74 ILE cc_start: 0.8775 (mm) cc_final: 0.8378 (mm) REVERT: B 528 MET cc_start: 0.8436 (mmm) cc_final: 0.8186 (mmm) REVERT: B 589 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8262 (ttpp) REVERT: D 162 MET cc_start: 0.8000 (mtp) cc_final: 0.7749 (mtp) REVERT: D 215 PHE cc_start: 0.7635 (m-80) cc_final: 0.7261 (m-80) REVERT: D 528 MET cc_start: 0.8596 (mmm) cc_final: 0.8227 (mmm) REVERT: E 294 MET cc_start: 0.8082 (tpt) cc_final: 0.7872 (tpp) REVERT: E 430 MET cc_start: 0.6341 (tmm) cc_final: 0.6019 (mtp) REVERT: E 664 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6124 (pm20) REVERT: F 143 MET cc_start: 0.5309 (OUTLIER) cc_final: 0.4884 (ppp) REVERT: F 221 SER cc_start: 0.3391 (OUTLIER) cc_final: 0.2896 (m) REVERT: F 263 ILE cc_start: 0.8202 (mt) cc_final: 0.7972 (mt) REVERT: C 495 MET cc_start: 0.8955 (ttp) cc_final: 0.8754 (ttp) REVERT: C 595 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7413 (mp0) outliers start: 68 outliers final: 58 residues processed: 246 average time/residue: 0.1807 time to fit residues: 78.4344 Evaluate side-chains 240 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 177 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 765 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 49 optimal weight: 10.0000 chunk 91 optimal weight: 0.1980 chunk 242 optimal weight: 0.8980 chunk 403 optimal weight: 6.9990 chunk 418 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 334 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 253 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.131888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093054 restraints weight = 73834.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090939 restraints weight = 55654.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.091494 restraints weight = 45685.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.091760 restraints weight = 38590.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091785 restraints weight = 36129.508| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34229 Z= 0.115 Angle : 0.584 12.158 46415 Z= 0.291 Chirality : 0.044 0.359 5370 Planarity : 0.004 0.063 5976 Dihedral : 8.422 88.407 5037 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.21 % Favored : 93.39 % Rotamer: Outliers : 1.92 % Allowed : 17.13 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.27 (0.13), residues: 4299 helix: 1.51 (0.13), residues: 1768 sheet: -0.36 (0.24), residues: 462 loop : -0.85 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 689 TYR 0.022 0.001 TYR D 680 PHE 0.026 0.001 PHE B 34 TRP 0.007 0.001 TRP A 515 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00263 (34229) covalent geometry : angle 0.58404 (46415) hydrogen bonds : bond 0.02964 ( 1285) hydrogen bonds : angle 4.14663 ( 3678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4648.52 seconds wall clock time: 82 minutes 3.13 seconds (4923.13 seconds total)