Starting phenix.real_space_refine on Mon Jul 6 06:28:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wbb_32396/07_2026/7wbb_32396.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbb_32396/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7wbb_32396/07_2026/7wbb_32396.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wbb_32396/07_2026/7wbb_32396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wbb_32396/07_2026/7wbb_32396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbb_32396/07_2026/7wbb_32396.map" model { file = "/net/cci-nas-00/data/ceres_data/7wbb_32396/07_2026/7wbb_32396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbb_32396/07_2026/7wbb_32396.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 8.21, per 1000 atoms: 0.24 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: 3.05 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: 1.28 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: 7.26 Time building geometry restraints manager: 4.03 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: 18740 17.86 - 35.71: 1773 35.71 - 53.57: 304 53.57 - 71.42: 38 71.42 - 89.28: 11 Dihedral angle restraints: 20866 sinusoidal: 8373 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 20863 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 32.870 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 13.738 89.278 12808 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/Z covalent geometry : bond 0.00228 / 0.14 (34229) covalent geometry : angle 0.55069 / 0.30 (46415) hydrogen bonds : bond 0.15291 / 10.73 ( 1285) hydrogen bonds : angle 5.67206 / 3.80 ( 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 : 1.400 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: 0.1855 time to fit residues: 107.1954 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 : 1.363 ------------------------------------------------------------------------------- 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... ** 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 149 GLN F 285 HIS C 231 GLN C 729 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.139083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100692 restraints weight = 74763.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099388 restraints weight = 65165.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.099565 restraints weight = 50032.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099821 restraints weight = 45763.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.100012 restraints weight = 39998.214| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34229 Z= 0.173 Angle : 0.588 9.798 46415 Z= 0.297 Chirality : 0.044 0.213 5370 Planarity : 0.004 0.055 5976 Dihedral : 4.970 72.614 4696 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.49 % Favored : 94.14 % Rotamer: Outliers : 1.02 % Allowed : 7.03 % Favored : 91.95 % 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: 0.72 (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 0.009 0.000 ARG A 434 TYR 0.018 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/Z covalent geometry : bond 0.00410 / 0.17 (34229) covalent geometry : angle 0.58772 / 0.30 (46415) hydrogen bonds : bond 0.03520 / 2.44 ( 1285) hydrogen bonds : angle 4.27654 / 2.90 ( 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 284 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6921 (pp20) REVERT: A 503 MET cc_start: 0.4956 (OUTLIER) cc_final: 0.3599 (pmm) REVERT: A 765 MET cc_start: 0.7841 (ptt) cc_final: 0.7552 (ptp) REVERT: E 162 MET cc_start: 0.8086 (mmt) cc_final: 0.7728 (mmt) REVERT: F 159 MET cc_start: 0.4164 (mmm) cc_final: 0.3776 (mmm) REVERT: F 544 ARG cc_start: 0.5485 (ptt180) cc_final: 0.5173 (mmm160) outliers start: 37 outliers final: 28 residues processed: 273 average time/residue: 0.1902 time to fit residues: 90.0885 Evaluate side-chains 240 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 503 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: 0.0670 chunk 377 optimal weight: 0.0010 chunk 379 optimal weight: 5.9990 chunk 351 optimal weight: 20.0000 chunk 274 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 179 optimal weight: 0.5980 chunk 239 optimal weight: 7.9990 chunk 28 optimal weight: 0.0170 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN D 660 ASN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.139015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101299 restraints weight = 74269.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.098192 restraints weight = 59757.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.098538 restraints weight = 49238.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.098710 restraints weight = 41616.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.098799 restraints weight = 40280.029| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34229 Z= 0.112 Angle : 0.527 10.636 46415 Z= 0.264 Chirality : 0.042 0.225 5370 Planarity : 0.004 0.054 5976 Dihedral : 4.969 74.103 4696 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.00 % Favored : 94.63 % Rotamer: Outliers : 1.24 % Allowed : 9.34 % Favored : 89.43 % 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: 0.78 (0.13), residues: 4299 helix: 1.80 (0.13), residues: 1762 sheet: 0.43 (0.26), residues: 449 loop : -0.57 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 462 TYR 0.032 0.001 TYR C 210 PHE 0.011 0.001 PHE C 215 TRP 0.004 0.001 TRP C 515 HIS 0.008 0.001 HIS F 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (34229) covalent geometry : angle 0.52735 / 0.26 (46415) hydrogen bonds : bond 0.02963 / 2.03 ( 1285) hydrogen bonds : angle 4.11179 / 2.79 ( 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 267 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.8121 (ppp) cc_final: 0.7472 (ppp) REVERT: A 765 MET cc_start: 0.8231 (ptt) cc_final: 0.7936 (ptp) REVERT: D 650 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8622 (pp) REVERT: E 430 MET cc_start: 0.4539 (tmm) cc_final: 0.3849 (mtm) REVERT: E 473 LEU cc_start: 0.8038 (tp) cc_final: 0.7830 (mp) REVERT: F 159 MET cc_start: 0.4037 (mmm) cc_final: 0.3742 (mmm) REVERT: C 294 MET cc_start: 0.8255 (ttm) cc_final: 0.7864 (ttm) outliers start: 45 outliers final: 35 residues processed: 253 average time/residue: 0.1658 time to fit residues: 73.9382 Evaluate side-chains 243 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE 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 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 272 SER 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 650 LEU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 261 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 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 553 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 159 optimal weight: 0.7980 chunk 77 optimal weight: 0.0570 chunk 234 optimal weight: 0.0670 chunk 39 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 380 optimal weight: 0.0770 chunk 18 optimal weight: 10.0000 chunk 340 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** D 122 GLN ** 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 = 0.4092 r_free = 0.4092 target = 0.137907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.100755 restraints weight = 73751.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.096711 restraints weight = 65905.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097408 restraints weight = 53220.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097652 restraints weight = 45665.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097783 restraints weight = 40173.363| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34229 Z= 0.112 Angle : 0.517 9.519 46415 Z= 0.259 Chirality : 0.042 0.175 5370 Planarity : 0.004 0.054 5976 Dihedral : 5.069 79.570 4696 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.65 % Favored : 93.98 % Rotamer: Outliers : 1.62 % Allowed : 10.87 % Favored : 87.51 % 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: 0.85 (0.13), residues: 4299 helix: 1.89 (0.13), residues: 1750 sheet: 0.39 (0.25), residues: 468 loop : -0.54 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 471 TYR 0.026 0.001 TYR C 210 PHE 0.017 0.001 PHE C 215 TRP 0.004 0.001 TRP C 515 HIS 0.007 0.001 HIS F 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (34229) covalent geometry : angle 0.51670 / 0.26 (46415) hydrogen bonds : bond 0.02723 / 1.86 ( 1285) hydrogen bonds : angle 3.97864 / 2.69 ( 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 276 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 1.356 Fit side-chains REVERT: A 257 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8821 (tt) REVERT: A 430 MET cc_start: 0.8067 (ppp) cc_final: 0.7432 (ppp) REVERT: A 765 MET cc_start: 0.8140 (ptt) cc_final: 0.7862 (ptp) REVERT: D 650 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8763 (pp) REVERT: E 430 MET cc_start: 0.5076 (tmm) cc_final: 0.4797 (tmm) REVERT: F 159 MET cc_start: 0.4252 (mmm) cc_final: 0.3891 (mmm) REVERT: C 294 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8196 (ttp) REVERT: C 595 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7270 (mp0) outliers start: 59 outliers final: 38 residues processed: 263 average time/residue: 0.1742 time to fit residues: 81.7705 Evaluate side-chains 240 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 656 VAL 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 362 VAL 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 147 VAL Chi-restraints excluded: chain D residue 276 VAL 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 650 LEU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN 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 390 ASN 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 595 GLU Chi-restraints excluded: chain C residue 612 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 117 optimal weight: 3.9990 chunk 281 optimal weight: 0.0040 chunk 310 optimal weight: 10.0000 chunk 393 optimal weight: 1.9990 chunk 269 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 380 optimal weight: 0.0170 chunk 31 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 137 optimal weight: 9.9990 overall best weight: 2.8036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN B 149 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 107 ASN F 166 ASN F 450 HIS C 77 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.134180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095541 restraints weight = 73622.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.092617 restraints weight = 72121.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092894 restraints weight = 54527.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094044 restraints weight = 45471.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.094026 restraints weight = 38500.889| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34229 Z= 0.168 Angle : 0.587 12.555 46415 Z= 0.296 Chirality : 0.044 0.168 5370 Planarity : 0.004 0.057 5976 Dihedral : 5.535 83.412 4696 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.72 % Favored : 93.91 % Rotamer: Outliers : 2.33 % Allowed : 12.14 % Favored : 85.53 % 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: 0.60 (0.13), residues: 4299 helix: 1.71 (0.13), residues: 1749 sheet: 0.30 (0.24), residues: 490 loop : -0.74 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 404 TYR 0.020 0.001 TYR D 768 PHE 0.016 0.001 PHE E 507 TRP 0.012 0.001 TRP C 515 HIS 0.014 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (34229) covalent geometry : angle 0.58734 / 0.30 (46415) hydrogen bonds : bond 0.03311 / 2.25 ( 1285) hydrogen bonds : angle 4.13428 / 2.80 ( 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 292 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 207 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.8248 (ppp) cc_final: 0.7472 (ppp) REVERT: B 528 MET cc_start: 0.8383 (mmm) cc_final: 0.8180 (mmm) REVERT: D 215 PHE cc_start: 0.7820 (m-80) cc_final: 0.7581 (m-80) REVERT: E 430 MET cc_start: 0.5861 (tmm) cc_final: 0.5550 (tmm) REVERT: E 435 HIS cc_start: 0.4616 (t70) cc_final: 0.4376 (t-90) REVERT: F 143 MET cc_start: 0.4269 (OUTLIER) cc_final: 0.3674 (ppp) REVERT: C 309 THR cc_start: 0.8753 (m) cc_final: 0.8311 (p) REVERT: C 514 TYR cc_start: 0.8117 (m-10) cc_final: 0.7905 (m-80) REVERT: C 595 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7087 (mp0) outliers start: 85 outliers final: 54 residues processed: 277 average time/residue: 0.1818 time to fit residues: 88.9266 Evaluate side-chains 246 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE 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 362 VAL 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 762 THR 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 178 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 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 261 ILE Chi-restraints excluded: chain E residue 277 SER 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 656 VAL Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 178 VAL 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 209 PHE 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 384 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 595 GLU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 307 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 385 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 369 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS A 266 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** 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 = 0.4036 r_free = 0.4036 target = 0.134124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.096311 restraints weight = 73409.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093479 restraints weight = 74402.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094346 restraints weight = 56328.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094660 restraints weight = 43284.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094718 restraints weight = 39665.742| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34229 Z= 0.143 Angle : 0.553 9.138 46415 Z= 0.277 Chirality : 0.043 0.224 5370 Planarity : 0.004 0.056 5976 Dihedral : 5.496 86.639 4696 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.68 % Favored : 93.95 % Rotamer: Outliers : 1.95 % Allowed : 13.45 % Favored : 84.60 % 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: 0.59 (0.13), residues: 4299 helix: 1.75 (0.13), residues: 1756 sheet: 0.20 (0.25), residues: 473 loop : -0.75 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 759 TYR 0.015 0.001 TYR C 210 PHE 0.021 0.001 PHE E 754 TRP 0.003 0.001 TRP A 515 HIS 0.010 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (34229) covalent geometry : angle 0.55310 / 0.28 (46415) hydrogen bonds : bond 0.02985 / 2.02 ( 1285) hydrogen bonds : angle 4.06199 / 2.75 ( 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 270 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 199 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.8178 (ppp) cc_final: 0.7413 (ppp) REVERT: D 80 LEU cc_start: 0.8756 (tt) cc_final: 0.8518 (mt) REVERT: D 215 PHE cc_start: 0.7933 (m-80) cc_final: 0.7622 (m-80) REVERT: E 294 MET cc_start: 0.8138 (tpt) cc_final: 0.7872 (tpp) REVERT: E 430 MET cc_start: 0.6083 (tmm) cc_final: 0.5854 (tmm) REVERT: E 664 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.5843 (pm20) REVERT: F 143 MET cc_start: 0.4453 (OUTLIER) cc_final: 0.3433 (ppp) REVERT: C 595 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7116 (mp0) outliers start: 71 outliers final: 54 residues processed: 254 average time/residue: 0.1693 time to fit residues: 76.9321 Evaluate side-chains 249 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 109 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 670 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 69 CYS 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 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 655 ILE Chi-restraints excluded: chain D residue 749 HIS 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 261 ILE Chi-restraints excluded: chain E residue 277 SER 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 F residue 94 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain C residue 64 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 197 optimal weight: 5.9990 chunk 15 optimal weight: 40.0000 chunk 224 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 297 optimal weight: 40.0000 chunk 295 optimal weight: 0.0070 chunk 44 optimal weight: 20.0000 chunk 341 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 338 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.134520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.096661 restraints weight = 73617.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095664 restraints weight = 64642.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.095225 restraints weight = 55371.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095571 restraints weight = 45932.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095707 restraints weight = 41417.613| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34229 Z= 0.116 Angle : 0.544 9.856 46415 Z= 0.271 Chirality : 0.042 0.200 5370 Planarity : 0.004 0.056 5976 Dihedral : 5.442 89.379 4696 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.68 % Favored : 93.95 % Rotamer: Outliers : 2.06 % Allowed : 13.65 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.13), residues: 4299 helix: 1.78 (0.13), residues: 1756 sheet: 0.14 (0.25), residues: 466 loop : -0.67 (0.14), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 429 TYR 0.013 0.001 TYR B 337 PHE 0.008 0.001 PHE E 507 TRP 0.004 0.001 TRP A 515 HIS 0.003 0.001 HIS E 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (34229) covalent geometry : angle 0.54440 / 0.27 (46415) hydrogen bonds : bond 0.02819 / 1.91 ( 1285) hydrogen bonds : angle 4.02106 / 2.73 ( 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 281 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 206 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 MET cc_start: 0.5431 (ttm) cc_final: 0.4567 (tmm) REVERT: A 430 MET cc_start: 0.8134 (ppp) cc_final: 0.7369 (ppp) REVERT: D 80 LEU cc_start: 0.8780 (tt) cc_final: 0.8541 (mt) REVERT: E 294 MET cc_start: 0.8058 (tpt) cc_final: 0.7802 (tpp) REVERT: E 430 MET cc_start: 0.6154 (tmm) cc_final: 0.5941 (tmm) REVERT: E 473 LEU cc_start: 0.8111 (tp) cc_final: 0.7760 (mp) REVERT: E 664 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.5847 (pm20) REVERT: F 143 MET cc_start: 0.4399 (OUTLIER) cc_final: 0.3883 (ppp) REVERT: F 263 ILE cc_start: 0.8083 (mt) cc_final: 0.7846 (mt) REVERT: C 595 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7245 (mp0) outliers start: 75 outliers final: 60 residues processed: 271 average time/residue: 0.1793 time to fit residues: 86.2051 Evaluate side-chains 258 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 195 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 647 VAL 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 670 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 69 CYS 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 406 ASP 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 180 ILE Chi-restraints excluded: chain E residue 261 ILE 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 E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 270 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 408 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN ** 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 = 0.4031 r_free = 0.4031 target = 0.133770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095331 restraints weight = 73782.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092210 restraints weight = 68738.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092696 restraints weight = 53303.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.093647 restraints weight = 43497.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093589 restraints weight = 37996.063| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34229 Z= 0.132 Angle : 0.563 13.925 46415 Z= 0.279 Chirality : 0.043 0.174 5370 Planarity : 0.004 0.057 5976 Dihedral : 5.486 87.587 4696 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.00 % Favored : 93.63 % Rotamer: Outliers : 2.11 % Allowed : 13.95 % Favored : 83.94 % 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: 0.59 (0.13), residues: 4299 helix: 1.74 (0.13), residues: 1760 sheet: 0.13 (0.25), residues: 460 loop : -0.73 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 748 TYR 0.014 0.001 TYR B 337 PHE 0.025 0.001 PHE E 754 TRP 0.004 0.001 TRP A 515 HIS 0.004 0.001 HIS C 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (34229) covalent geometry : angle 0.56318 / 0.28 (46415) hydrogen bonds : bond 0.02924 / 1.99 ( 1285) hydrogen bonds : angle 4.03176 / 2.73 ( 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 276 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 199 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 MET cc_start: 0.5388 (ttm) cc_final: 0.4506 (tmm) REVERT: A 430 MET cc_start: 0.8155 (ppp) cc_final: 0.7385 (ppp) REVERT: D 80 LEU cc_start: 0.8848 (tt) cc_final: 0.8568 (mt) REVERT: E 33 GLU cc_start: 0.7854 (tp30) cc_final: 0.7572 (tp30) REVERT: E 294 MET cc_start: 0.8109 (tpt) cc_final: 0.7851 (tpp) REVERT: E 430 MET cc_start: 0.6246 (tmm) cc_final: 0.5974 (tmm) REVERT: E 664 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.5950 (pm20) REVERT: F 143 MET cc_start: 0.4425 (OUTLIER) cc_final: 0.3877 (ppp) REVERT: F 263 ILE cc_start: 0.8145 (mt) cc_final: 0.7907 (mt) REVERT: C 595 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7170 (mp0) outliers start: 77 outliers final: 65 residues processed: 264 average time/residue: 0.1772 time to fit residues: 81.9750 Evaluate side-chains 258 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 190 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 109 ILE 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 670 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 69 CYS 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 406 ASP 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 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 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 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 178 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 327 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 366 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 392 optimal weight: 6.9990 chunk 271 optimal weight: 0.0670 chunk 316 optimal weight: 0.0170 chunk 389 optimal weight: 8.9990 chunk 11 optimal weight: 0.0370 chunk 283 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 402 optimal weight: 1.9990 overall best weight: 1.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.133964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.096190 restraints weight = 73504.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093424 restraints weight = 69992.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094139 restraints weight = 56421.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094503 restraints weight = 43162.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094555 restraints weight = 39032.288| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34229 Z= 0.120 Angle : 0.563 12.334 46415 Z= 0.278 Chirality : 0.043 0.169 5370 Planarity : 0.004 0.057 5976 Dihedral : 5.439 84.374 4696 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.61 % Favored : 94.02 % Rotamer: Outliers : 2.09 % Allowed : 14.55 % Favored : 83.36 % 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: 0.59 (0.13), residues: 4299 helix: 1.73 (0.13), residues: 1762 sheet: 0.12 (0.25), residues: 460 loop : -0.71 (0.14), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 677 TYR 0.015 0.001 TYR C 210 PHE 0.021 0.001 PHE E 754 TRP 0.005 0.001 TRP A 515 HIS 0.004 0.001 HIS E 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (34229) covalent geometry : angle 0.56272 / 0.28 (46415) hydrogen bonds : bond 0.02850 / 1.93 ( 1285) hydrogen bonds : angle 4.03769 / 2.74 ( 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 271 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 195 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 MET cc_start: 0.5336 (ttm) cc_final: 0.4486 (tmm) REVERT: A 430 MET cc_start: 0.8105 (ppp) cc_final: 0.7337 (ppp) REVERT: D 528 MET cc_start: 0.8737 (mmm) cc_final: 0.8407 (mmm) REVERT: E 33 GLU cc_start: 0.7847 (tp30) cc_final: 0.7569 (tp30) REVERT: E 294 MET cc_start: 0.8069 (tpt) cc_final: 0.7796 (tpp) REVERT: E 430 MET cc_start: 0.6293 (tmm) cc_final: 0.6044 (tmm) REVERT: E 664 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.5903 (pm20) REVERT: F 143 MET cc_start: 0.4765 (OUTLIER) cc_final: 0.4276 (ppp) REVERT: F 263 ILE cc_start: 0.8111 (mt) cc_final: 0.7871 (mt) outliers start: 76 outliers final: 67 residues processed: 260 average time/residue: 0.1643 time to fit residues: 75.6159 Evaluate side-chains 261 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 192 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 109 ILE 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 473 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 69 CYS 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 406 ASP 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 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 566 THR 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 143 MET Chi-restraints excluded: chain F residue 178 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 203 optimal weight: 4.9990 chunk 356 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 347 optimal weight: 0.2980 chunk 214 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 317 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** 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 = 0.4032 r_free = 0.4032 target = 0.133844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.096167 restraints weight = 73937.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093227 restraints weight = 72469.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093909 restraints weight = 54450.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094934 restraints weight = 42961.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094866 restraints weight = 37413.314| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34229 Z= 0.120 Angle : 0.564 12.277 46415 Z= 0.277 Chirality : 0.043 0.172 5370 Planarity : 0.004 0.058 5976 Dihedral : 5.444 81.892 4696 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.84 % Favored : 93.79 % Rotamer: Outliers : 2.06 % Allowed : 14.58 % Favored : 83.36 % 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: 0.61 (0.13), residues: 4299 helix: 1.74 (0.13), residues: 1764 sheet: 0.12 (0.25), residues: 460 loop : -0.70 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 677 TYR 0.014 0.001 TYR B 210 PHE 0.022 0.001 PHE E 754 TRP 0.006 0.001 TRP A 515 HIS 0.004 0.001 HIS E 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (34229) covalent geometry : angle 0.56447 / 0.28 (46415) hydrogen bonds : bond 0.02821 / 1.91 ( 1285) hydrogen bonds : angle 4.01250 / 2.72 ( 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 271 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 196 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 MET cc_start: 0.5113 (ttm) cc_final: 0.4314 (tmm) REVERT: A 430 MET cc_start: 0.8088 (ppp) cc_final: 0.7306 (ppp) REVERT: D 80 LEU cc_start: 0.8395 (mp) cc_final: 0.8102 (mt) REVERT: D 215 PHE cc_start: 0.7850 (m-80) cc_final: 0.7614 (m-80) REVERT: D 528 MET cc_start: 0.8705 (mmm) cc_final: 0.8383 (mmm) REVERT: E 33 GLU cc_start: 0.7835 (tp30) cc_final: 0.7578 (tp30) REVERT: E 294 MET cc_start: 0.8055 (tpt) cc_final: 0.7810 (tpp) REVERT: E 430 MET cc_start: 0.6323 (tmm) cc_final: 0.6031 (tmm) REVERT: E 507 PHE cc_start: 0.3548 (t80) cc_final: 0.3258 (t80) REVERT: E 664 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.5962 (pm20) REVERT: F 143 MET cc_start: 0.4975 (OUTLIER) cc_final: 0.4474 (ppp) REVERT: F 263 ILE cc_start: 0.8068 (mt) cc_final: 0.7837 (mt) outliers start: 75 outliers final: 65 residues processed: 259 average time/residue: 0.1854 time to fit residues: 85.0090 Evaluate side-chains 258 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 191 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 109 ILE 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 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 762 THR 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 178 VAL Chi-restraints excluded: chain D residue 276 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 406 ASP 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 F residue 94 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 178 VAL 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 327 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 242 optimal weight: 0.0770 chunk 403 optimal weight: 0.8980 chunk 418 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 334 optimal weight: 6.9990 chunk 161 optimal weight: 40.0000 chunk 9 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 HIS ** 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 = 0.4019 r_free = 0.4019 target = 0.132960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096119 restraints weight = 73487.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092467 restraints weight = 68563.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.092501 restraints weight = 61356.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093364 restraints weight = 49723.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.093474 restraints weight = 42073.689| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3527 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= 0.139 Angle : 0.582 11.875 46415 Z= 0.286 Chirality : 0.043 0.171 5370 Planarity : 0.004 0.058 5976 Dihedral : 5.496 77.823 4696 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.89 % Favored : 93.74 % Rotamer: Outliers : 2.03 % Allowed : 14.77 % Favored : 83.20 % 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: 0.56 (0.13), residues: 4299 helix: 1.70 (0.13), residues: 1767 sheet: 0.09 (0.25), residues: 460 loop : -0.73 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 113 TYR 0.014 0.001 TYR B 337 PHE 0.021 0.001 PHE E 754 TRP 0.005 0.001 TRP C 515 HIS 0.013 0.001 HIS E 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (34229) covalent geometry : angle 0.58199 / 0.29 (46415) hydrogen bonds : bond 0.02970 / 2.01 ( 1285) hydrogen bonds : angle 4.05659 / 2.75 ( 3678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4653.35 seconds wall clock time: 81 minutes 57.60 seconds (4917.60 seconds total)