Starting phenix.real_space_refine on Sat Jun 28 19:48:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wbb_32396/06_2025/7wbb_32396.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbb_32396/06_2025/7wbb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wbb_32396/06_2025/7wbb_32396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbb_32396/06_2025/7wbb_32396.map" model { file = "/net/cci-nas-00/data/ceres_data/7wbb_32396/06_2025/7wbb_32396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbb_32396/06_2025/7wbb_32396.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.83, per 1000 atoms: 0.59 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: 9.23 Conformation dependent library (CDL) restraints added in 4.5 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: 4.45 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: 13.15 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5748 1.31 - 1.43: 8077 1.43 - 1.56: 20129 1.56 - 1.69: 55 1.69 - 1.82: 220 Bond restraints: 34229 Sorted by residual: bond pdb=" C PRO A 264 " pdb=" O PRO A 264 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" N LYS B 563 " pdb=" CA LYS B 563 " ideal model delta sigma weight residual 1.459 1.498 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ILE A 261 " pdb=" CA ILE A 261 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N GLY A 248 " pdb=" CA GLY A 248 " ideal model delta sigma weight residual 1.444 1.475 -0.032 1.02e-02 9.61e+03 9.55e+00 bond pdb=" N SER B 562 " pdb=" CA SER B 562 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.32e+00 ... (remaining 34224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 45673 2.04 - 4.08: 647 4.08 - 6.12: 77 6.12 - 8.17: 11 8.17 - 10.21: 7 Bond angle restraints: 46415 Sorted by residual: angle pdb=" C LYS B 563 " pdb=" N THR B 564 " pdb=" CA THR B 564 " ideal model delta sigma weight residual 120.29 129.36 -9.07 1.42e+00 4.96e-01 4.08e+01 angle pdb=" C SER E 432 " pdb=" N ASP E 433 " pdb=" CA ASP E 433 " ideal model delta sigma weight residual 123.91 134.12 -10.21 1.66e+00 3.63e-01 3.78e+01 angle pdb=" C ILE A 261 " pdb=" N GLU A 262 " pdb=" CA GLU A 262 " ideal model delta sigma weight residual 120.29 128.54 -8.25 1.42e+00 4.96e-01 3.37e+01 angle pdb=" O ILE A 261 " pdb=" C ILE A 261 " pdb=" N GLU A 262 " ideal model delta sigma weight residual 121.83 127.22 -5.39 1.03e+00 9.43e-01 2.74e+01 angle pdb=" N LYS B 563 " pdb=" CA LYS B 563 " pdb=" C LYS B 563 " ideal model delta sigma weight residual 111.07 116.32 -5.25 1.07e+00 8.73e-01 2.41e+01 ... (remaining 46410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 18833 17.86 - 35.71: 1875 35.71 - 53.57: 430 53.57 - 71.42: 51 71.42 - 89.28: 18 Dihedral angle restraints: 21207 sinusoidal: 8714 harmonic: 12493 Sorted by residual: dihedral pdb=" C LYS E 563 " pdb=" N LYS E 563 " pdb=" CA LYS E 563 " pdb=" CB LYS E 563 " ideal model delta harmonic sigma weight residual -122.60 -133.85 11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CA SER E 99 " pdb=" C SER E 99 " pdb=" N THR E 100 " pdb=" CA THR E 100 " ideal model delta harmonic sigma weight residual 180.00 158.69 21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" N LYS E 563 " pdb=" C LYS E 563 " pdb=" CA LYS E 563 " pdb=" CB LYS E 563 " ideal model delta harmonic sigma weight residual 122.80 132.13 -9.33 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 21204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4755 0.068 - 0.136: 588 0.136 - 0.205: 21 0.205 - 0.273: 4 0.273 - 0.341: 2 Chirality restraints: 5370 Sorted by residual: chirality pdb=" CA LYS E 563 " pdb=" N LYS E 563 " pdb=" C LYS E 563 " pdb=" CB LYS E 563 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA THR E 564 " pdb=" N THR E 564 " pdb=" C THR E 564 " pdb=" CB THR E 564 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CB ILE C 310 " pdb=" CA ILE C 310 " pdb=" CG1 ILE C 310 " pdb=" CG2 ILE C 310 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 5367 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 609 " 0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 610 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 261 " -0.013 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C ILE A 261 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 261 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 262 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 432 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C SER E 432 " -0.047 2.00e-02 2.50e+03 pdb=" O SER E 432 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E 433 " 0.015 2.00e-02 2.50e+03 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3177 2.75 - 3.28: 34205 3.28 - 3.82: 55315 3.82 - 4.36: 60892 4.36 - 4.90: 105370 Nonbonded interactions: 258959 Sorted by model distance: nonbonded pdb=" OD1 ASP C 456 " pdb=" OG SER C 501 " model vdw 2.206 3.040 nonbonded pdb=" O ASN E 660 " pdb=" OH TYR E 769 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 720 " pdb=" OE1 GLU A 723 " model vdw 2.229 3.040 nonbonded pdb=" O ASN E 577 " pdb=" OG SER E 611 " model vdw 2.233 3.040 nonbonded pdb=" O ALA E 334 " pdb=" OG SER E 340 " model vdw 2.239 3.040 ... (remaining 258954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 777 or resid 801)) selection = (chain 'B' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 777 or resid 801)) selection = (chain 'C' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 777 or resid 801)) selection = (chain 'D' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 777 or resid 801)) selection = (chain 'E' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 777 or resid 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.050 Extract box with map and model: 1.340 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 78.390 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.150 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 34229 Z= 0.141 Angle : 0.551 10.207 46415 Z= 0.302 Chirality : 0.043 0.341 5370 Planarity : 0.004 0.088 5976 Dihedral : 14.717 89.278 13149 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (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 TRP 0.003 0.000 TRP D 515 HIS 0.007 0.000 HIS F 450 PHE 0.017 0.001 PHE B 274 TYR 0.012 0.000 TYR A 337 ARG 0.005 0.000 ARG F 328 Details of bonding type rmsd hydrogen bonds : bond 0.15291 ( 1285) hydrogen bonds : angle 5.67206 ( 3678) covalent geometry : bond 0.00228 (34229) covalent geometry : angle 0.55069 (46415) *********************** 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 : 3.925 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: 0.3993 time to fit residues: 231.0583 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 : 4.145 ------------------------------------------------------------------------------- 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 363 optimal weight: 0.8980 chunk 326 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 337 optimal weight: 50.0000 chunk 130 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 391 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN B 44 HIS D 407 GLN D 660 ASN D 729 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN F 166 ASN F 285 HIS ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN C 729 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.135542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.097707 restraints weight = 73767.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095228 restraints weight = 76473.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095559 restraints weight = 55111.860| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 34229 Z= 0.234 Angle : 0.664 8.794 46415 Z= 0.340 Chirality : 0.046 0.242 5370 Planarity : 0.005 0.060 5976 Dihedral : 9.358 89.221 5037 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.93 % Favored : 93.72 % Rotamer: Outliers : 1.24 % Allowed : 7.74 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.13), residues: 4299 helix: 1.49 (0.13), residues: 1747 sheet: 0.47 (0.25), residues: 462 loop : -0.66 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 515 HIS 0.013 0.001 HIS A 266 PHE 0.019 0.002 PHE B 274 TYR 0.021 0.002 TYR D 52 ARG 0.006 0.001 ARG F 404 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 1285) hydrogen bonds : angle 4.47886 ( 3678) covalent geometry : bond 0.00547 (34229) covalent geometry : angle 0.66355 (46415) *********************** 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 276 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 3.697 Fit side-chains REVERT: A 503 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.3822 (pmm) REVERT: A 765 MET cc_start: 0.8187 (ptt) cc_final: 0.7902 (ptp) REVERT: B 151 LEU cc_start: 0.7297 (pt) cc_final: 0.7082 (pt) REVERT: B 740 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7712 (tp) REVERT: E 143 MET cc_start: 0.4533 (tmm) cc_final: 0.3485 (tmm) REVERT: F 261 ILE cc_start: 0.8691 (pt) cc_final: 0.8463 (mt) REVERT: C 456 ASP cc_start: 0.8370 (m-30) cc_final: 0.8108 (m-30) outliers start: 45 outliers final: 34 residues processed: 265 average time/residue: 0.4009 time to fit residues: 183.6035 Evaluate side-chains 231 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU 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 437 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR 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 581 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 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 F residue 94 ASN Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain C residue 64 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 513 VAL Chi-restraints excluded: chain C residue 676 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 5 optimal weight: 40.0000 chunk 99 optimal weight: 2.9990 chunk 303 optimal weight: 8.9990 chunk 394 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 424 optimal weight: 8.9990 chunk 196 optimal weight: 0.6980 chunk 30 optimal weight: 50.0000 chunk 26 optimal weight: 0.0060 chunk 98 optimal weight: 3.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 266 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4077 r_free = 0.4077 target = 0.136892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.097757 restraints weight = 74130.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096345 restraints weight = 62274.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096915 restraints weight = 45084.352| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2092 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= 0.111 Angle : 0.541 9.767 46415 Z= 0.272 Chirality : 0.042 0.176 5370 Planarity : 0.004 0.054 5976 Dihedral : 9.288 89.423 5037 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.95 % Favored : 94.70 % Rotamer: Outliers : 1.37 % Allowed : 10.24 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 4299 helix: 1.70 (0.13), residues: 1751 sheet: 0.37 (0.25), residues: 462 loop : -0.63 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 515 HIS 0.009 0.001 HIS F 450 PHE 0.010 0.001 PHE A 602 TYR 0.013 0.001 TYR B 337 ARG 0.004 0.000 ARG E 471 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 1285) hydrogen bonds : angle 4.18651 ( 3678) covalent geometry : bond 0.00250 (34229) covalent geometry : angle 0.54053 (46415) *********************** 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 260 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 3.787 Fit side-chains revert: symmetry clash REVERT: A 263 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6587 (mm) REVERT: A 430 MET cc_start: 0.8092 (ppp) cc_final: 0.7432 (ppp) REVERT: A 765 MET cc_start: 0.8308 (ptt) cc_final: 0.7976 (ptp) REVERT: D 770 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: E 473 LEU cc_start: 0.8040 (tp) cc_final: 0.7838 (mp) REVERT: F 430 MET cc_start: 0.4928 (ptm) cc_final: 0.4026 (ttp) REVERT: C 456 ASP cc_start: 0.8367 (m-30) cc_final: 0.7909 (m-30) REVERT: C 514 TYR cc_start: 0.8078 (m-10) cc_final: 0.7859 (m-80) REVERT: C 595 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7179 (mp0) outliers start: 50 outliers final: 32 residues processed: 248 average time/residue: 0.3999 time to fit residues: 172.7595 Evaluate side-chains 218 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 350 ILE 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 95 VAL 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 749 HIS Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain E residue 69 CYS 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 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 362 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 612 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 261 optimal weight: 20.0000 chunk 351 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 384 optimal weight: 0.4980 chunk 243 optimal weight: 0.0270 chunk 289 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 18 optimal weight: 40.0000 chunk 100 optimal weight: 0.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.137257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099892 restraints weight = 74086.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.097694 restraints weight = 67350.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097712 restraints weight = 55066.502| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34229 Z= 0.100 Angle : 0.520 9.497 46415 Z= 0.262 Chirality : 0.042 0.192 5370 Planarity : 0.004 0.053 5976 Dihedral : 9.052 87.113 5037 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.63 % Favored : 94.02 % Rotamer: Outliers : 1.51 % Allowed : 11.37 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.13), residues: 4299 helix: 1.81 (0.13), residues: 1745 sheet: 0.32 (0.25), residues: 467 loop : -0.61 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 515 HIS 0.007 0.001 HIS F 450 PHE 0.011 0.001 PHE C 215 TYR 0.021 0.001 TYR C 210 ARG 0.004 0.000 ARG C 429 Details of bonding type rmsd hydrogen bonds : bond 0.02774 ( 1285) hydrogen bonds : angle 4.02162 ( 3678) covalent geometry : bond 0.00223 (34229) covalent geometry : angle 0.51969 (46415) *********************** 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 261 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 4.025 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.8035 (ppp) cc_final: 0.7399 (ppp) REVERT: A 765 MET cc_start: 0.8270 (ptt) cc_final: 0.7924 (ptp) REVERT: B 770 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7212 (pp20) REVERT: D 131 VAL cc_start: 0.8192 (t) cc_final: 0.7880 (m) REVERT: D 770 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: E 430 MET cc_start: 0.4964 (tmm) cc_final: 0.4737 (tmm) REVERT: F 162 MET cc_start: 0.6319 (mmm) cc_final: 0.6056 (mmm) REVERT: F 430 MET cc_start: 0.4838 (ptm) cc_final: 0.4404 (ttp) REVERT: C 456 ASP cc_start: 0.8390 (m-30) cc_final: 0.7962 (m-30) REVERT: C 595 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7207 (mp0) outliers start: 55 outliers final: 34 residues processed: 249 average time/residue: 0.4029 time to fit residues: 176.3974 Evaluate side-chains 230 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 269 THR 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 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 406 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 653 VAL 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 383 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 595 GLU Chi-restraints excluded: chain C residue 598 ILE 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 187 optimal weight: 9.9990 chunk 396 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 chunk 139 optimal weight: 3.9990 chunk 264 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 407 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 678 HIS F 450 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.135653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.095170 restraints weight = 73299.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093289 restraints weight = 69559.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093550 restraints weight = 46887.425| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34229 Z= 0.123 Angle : 0.530 9.278 46415 Z= 0.268 Chirality : 0.042 0.174 5370 Planarity : 0.004 0.055 5976 Dihedral : 8.781 85.857 5037 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.65 % Favored : 93.98 % Rotamer: Outliers : 2.20 % Allowed : 11.75 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.13), residues: 4299 helix: 1.81 (0.13), residues: 1746 sheet: 0.27 (0.25), residues: 449 loop : -0.65 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 515 HIS 0.006 0.001 HIS F 450 PHE 0.016 0.001 PHE E 507 TYR 0.026 0.001 TYR C 210 ARG 0.003 0.000 ARG C 429 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 1285) hydrogen bonds : angle 3.98063 ( 3678) covalent geometry : bond 0.00287 (34229) covalent geometry : angle 0.53025 (46415) *********************** 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 280 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 3.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.8210 (ppp) cc_final: 0.7544 (ppp) REVERT: B 330 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8553 (mt) REVERT: B 770 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7238 (pp20) REVERT: E 430 MET cc_start: 0.5624 (tmm) cc_final: 0.5353 (tmm) REVERT: E 473 LEU cc_start: 0.8167 (tp) cc_final: 0.7800 (mp) REVERT: F 143 MET cc_start: 0.4165 (OUTLIER) cc_final: 0.3579 (ppp) REVERT: F 162 MET cc_start: 0.6745 (mmm) cc_final: 0.6477 (mmm) REVERT: F 430 MET cc_start: 0.4887 (ptm) cc_final: 0.4514 (ttp) outliers start: 80 outliers final: 51 residues processed: 266 average time/residue: 0.3783 time to fit residues: 177.0588 Evaluate side-chains 243 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 3.637 ------------------------------------------------------------------------------- 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 561 CYS 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 290 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 330 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 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 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 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 436 VAL 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 143 MET 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 11 optimal weight: 8.9990 chunk 284 optimal weight: 20.0000 chunk 429 optimal weight: 3.9990 chunk 349 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 379 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 339 optimal weight: 40.0000 chunk 282 optimal weight: 2.9990 chunk 283 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN D 91 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 107 ASN C 77 ASN C 450 HIS ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.129968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090897 restraints weight = 73943.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088027 restraints weight = 67993.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088803 restraints weight = 53230.186| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 34229 Z= 0.293 Angle : 0.702 10.208 46415 Z= 0.358 Chirality : 0.047 0.184 5370 Planarity : 0.005 0.068 5976 Dihedral : 9.178 87.952 5037 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.44 % Favored : 93.14 % Rotamer: Outliers : 2.22 % Allowed : 13.34 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.13), residues: 4299 helix: 1.27 (0.12), residues: 1753 sheet: 0.05 (0.24), residues: 479 loop : -0.95 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 515 HIS 0.011 0.002 HIS E 39 PHE 0.021 0.002 PHE E 507 TYR 0.033 0.002 TYR D 768 ARG 0.008 0.001 ARG C 419 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 1285) hydrogen bonds : angle 4.52085 ( 3678) covalent geometry : bond 0.00698 (34229) covalent geometry : angle 0.70153 (46415) *********************** 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 280 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 199 time to evaluate : 3.998 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.8290 (ppp) cc_final: 0.7430 (ppp) REVERT: B 42 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7767 (mtmt) REVERT: B 74 ILE cc_start: 0.8777 (mm) cc_final: 0.8351 (mm) REVERT: D 80 LEU cc_start: 0.8544 (mp) cc_final: 0.8331 (mt) REVERT: D 215 PHE cc_start: 0.7940 (m-80) cc_final: 0.7552 (m-80) REVERT: E 223 HIS cc_start: 0.7875 (m-70) cc_final: 0.7669 (m-70) REVERT: E 664 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: E 748 ARG cc_start: 0.7463 (tpm170) cc_final: 0.7253 (tpm170) REVERT: F 137 TYR cc_start: 0.4839 (m-10) cc_final: 0.4579 (m-10) REVERT: F 143 MET cc_start: 0.5023 (OUTLIER) cc_final: 0.3947 (ppp) REVERT: F 263 ILE cc_start: 0.8196 (mt) cc_final: 0.7943 (mt) REVERT: F 430 MET cc_start: 0.5105 (ptm) cc_final: 0.4891 (ttp) REVERT: C 294 MET cc_start: 0.8447 (ttm) cc_final: 0.8206 (ttm) REVERT: C 488 LEU cc_start: 0.9118 (tp) cc_final: 0.8775 (tp) outliers start: 81 outliers final: 62 residues processed: 270 average time/residue: 0.4004 time to fit residues: 186.7257 Evaluate side-chains 242 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 290 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 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 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 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 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 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 598 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 201 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 314 optimal weight: 0.9980 chunk 320 optimal weight: 2.9990 chunk 352 optimal weight: 20.0000 chunk 250 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 211 optimal weight: 5.9990 chunk 282 optimal weight: 8.9990 chunk 280 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4002 r_free = 0.4002 target = 0.131848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092858 restraints weight = 73859.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090943 restraints weight = 69894.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091191 restraints weight = 55203.032| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34229 Z= 0.142 Angle : 0.581 10.299 46415 Z= 0.293 Chirality : 0.043 0.173 5370 Planarity : 0.004 0.059 5976 Dihedral : 8.883 84.258 5037 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.61 % Favored : 93.98 % Rotamer: Outliers : 2.03 % Allowed : 14.72 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.13), residues: 4299 helix: 1.48 (0.13), residues: 1765 sheet: 0.02 (0.24), residues: 485 loop : -0.89 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 515 HIS 0.005 0.001 HIS C 44 PHE 0.022 0.001 PHE E 754 TYR 0.016 0.001 TYR C 210 ARG 0.015 0.000 ARG E 689 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 1285) hydrogen bonds : angle 4.25743 ( 3678) covalent geometry : bond 0.00334 (34229) covalent geometry : angle 0.58077 (46415) *********************** 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 267 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 193 time to evaluate : 3.554 Fit side-chains REVERT: A 140 LEU cc_start: 0.3804 (pt) cc_final: 0.2912 (tp) REVERT: A 430 MET cc_start: 0.8302 (ppp) cc_final: 0.7452 (ppp) REVERT: B 42 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7861 (mtmt) REVERT: B 74 ILE cc_start: 0.8728 (mm) cc_final: 0.8315 (mm) REVERT: E 223 HIS cc_start: 0.7926 (m-70) cc_final: 0.7698 (m-70) REVERT: E 430 MET cc_start: 0.6056 (tmm) cc_final: 0.5543 (mtm) REVERT: F 137 TYR cc_start: 0.4964 (m-10) cc_final: 0.4733 (m-10) REVERT: F 143 MET cc_start: 0.4792 (OUTLIER) cc_final: 0.4350 (ppp) REVERT: F 263 ILE cc_start: 0.8225 (mt) cc_final: 0.7968 (mt) REVERT: C 460 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9167 (tt) outliers start: 74 outliers final: 55 residues processed: 256 average time/residue: 0.3848 time to fit residues: 171.1830 Evaluate side-chains 242 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 3.635 ------------------------------------------------------------------------------- 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 561 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 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 740 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 622 SER 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 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 406 ASP Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 762 THR 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 276 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 496 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 401 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 354 optimal weight: 0.3980 chunk 186 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 389 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 244 optimal weight: 0.3980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** 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 = 0.4003 r_free = 0.4003 target = 0.131934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093333 restraints weight = 73093.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091926 restraints weight = 52838.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092444 restraints weight = 48022.283| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34229 Z= 0.142 Angle : 0.580 11.497 46415 Z= 0.290 Chirality : 0.043 0.236 5370 Planarity : 0.004 0.066 5976 Dihedral : 8.708 83.789 5037 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.23 % Favored : 93.37 % Rotamer: Outliers : 2.14 % Allowed : 14.83 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.13), residues: 4299 helix: 1.54 (0.13), residues: 1766 sheet: -0.04 (0.24), residues: 491 loop : -0.87 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 515 HIS 0.004 0.001 HIS E 306 PHE 0.020 0.001 PHE E 754 TYR 0.016 0.001 TYR B 210 ARG 0.010 0.000 ARG E 689 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 1285) hydrogen bonds : angle 4.17024 ( 3678) covalent geometry : bond 0.00335 (34229) covalent geometry : angle 0.58042 (46415) *********************** 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 275 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 197 time to evaluate : 3.727 Fit side-chains REVERT: A 140 LEU cc_start: 0.3658 (pt) cc_final: 0.2828 (tp) REVERT: A 430 MET cc_start: 0.8195 (ppp) cc_final: 0.7370 (ppp) REVERT: B 42 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7810 (mtmt) REVERT: B 74 ILE cc_start: 0.8712 (mm) cc_final: 0.8307 (mm) REVERT: E 614 PHE cc_start: 0.8157 (t80) cc_final: 0.7939 (t80) REVERT: E 748 ARG cc_start: 0.7299 (tpm170) cc_final: 0.6929 (tpm170) REVERT: F 143 MET cc_start: 0.4972 (OUTLIER) cc_final: 0.4511 (ppp) REVERT: F 263 ILE cc_start: 0.8096 (mt) cc_final: 0.7856 (mt) REVERT: F 765 MET cc_start: 0.1410 (ttt) cc_final: 0.0939 (ttt) REVERT: C 53 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8445 (mt) REVERT: C 460 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9147 (tt) outliers start: 78 outliers final: 64 residues processed: 267 average time/residue: 0.3980 time to fit residues: 185.9646 Evaluate side-chains 255 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 188 time to evaluate : 3.636 ------------------------------------------------------------------------------- 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 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain 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 290 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 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 362 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 622 SER 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 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 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 461 CYS Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 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 C residue 36 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 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 460 LEU 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 Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 382 optimal weight: 0.0770 chunk 163 optimal weight: 0.0000 chunk 206 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 368 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 380 optimal weight: 0.0980 overall best weight: 0.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN C 642 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.134154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.095585 restraints weight = 73617.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.093402 restraints weight = 52766.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094358 restraints weight = 42472.166| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 34229 Z= 0.102 Angle : 0.561 11.708 46415 Z= 0.280 Chirality : 0.042 0.321 5370 Planarity : 0.004 0.062 5976 Dihedral : 8.408 87.754 5037 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.58 % Favored : 94.05 % Rotamer: Outliers : 1.67 % Allowed : 15.46 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4299 helix: 1.67 (0.13), residues: 1764 sheet: -0.07 (0.25), residues: 458 loop : -0.78 (0.14), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 515 HIS 0.003 0.001 HIS E 223 PHE 0.019 0.001 PHE E 754 TYR 0.015 0.001 TYR B 210 ARG 0.011 0.000 ARG E 689 Details of bonding type rmsd hydrogen bonds : bond 0.02692 ( 1285) hydrogen bonds : angle 4.04822 ( 3678) covalent geometry : bond 0.00220 (34229) covalent geometry : angle 0.56099 (46415) *********************** 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 269 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 4.161 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.3595 (pt) cc_final: 0.2827 (tp) REVERT: A 430 MET cc_start: 0.8072 (ppp) cc_final: 0.7279 (ppp) REVERT: B 42 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7785 (mtmt) REVERT: B 74 ILE cc_start: 0.8597 (mm) cc_final: 0.8121 (mm) REVERT: D 80 LEU cc_start: 0.8797 (tt) cc_final: 0.8555 (mt) REVERT: D 215 PHE cc_start: 0.7613 (m-80) cc_final: 0.7256 (m-80) REVERT: D 528 MET cc_start: 0.8656 (mmm) cc_final: 0.8302 (mmm) REVERT: E 181 THR cc_start: 0.5906 (m) cc_final: 0.5339 (p) REVERT: E 430 MET cc_start: 0.6370 (tmm) cc_final: 0.5546 (mtm) REVERT: E 614 PHE cc_start: 0.8137 (t80) cc_final: 0.7926 (t80) REVERT: E 748 ARG cc_start: 0.7389 (tpm170) cc_final: 0.7029 (tpm170) REVERT: F 143 MET cc_start: 0.4858 (OUTLIER) cc_final: 0.4368 (ppp) REVERT: F 263 ILE cc_start: 0.8138 (mt) cc_final: 0.7902 (mt) REVERT: C 456 ASP cc_start: 0.8277 (m-30) cc_final: 0.8021 (m-30) outliers start: 61 outliers final: 50 residues processed: 262 average time/residue: 0.4032 time to fit residues: 186.9767 Evaluate side-chains 245 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 3.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 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 261 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 622 SER Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 461 CYS Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 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 458 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 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 612 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 400 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 227 optimal weight: 0.6980 chunk 415 optimal weight: 2.9990 chunk 206 optimal weight: 0.0770 chunk 379 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.134054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099128 restraints weight = 73491.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.097321 restraints weight = 87545.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098337 restraints weight = 81234.562| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34229 Z= 0.102 Angle : 0.563 11.730 46415 Z= 0.279 Chirality : 0.042 0.317 5370 Planarity : 0.004 0.061 5976 Dihedral : 8.218 85.305 5037 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.89 % Favored : 93.74 % Rotamer: Outliers : 1.81 % Allowed : 15.76 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.13), residues: 4299 helix: 1.68 (0.13), residues: 1766 sheet: -0.08 (0.25), residues: 460 loop : -0.76 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 515 HIS 0.016 0.001 HIS E 435 PHE 0.019 0.001 PHE E 507 TYR 0.012 0.001 TYR B 337 ARG 0.005 0.000 ARG E 689 Details of bonding type rmsd hydrogen bonds : bond 0.02668 ( 1285) hydrogen bonds : angle 3.99691 ( 3678) covalent geometry : bond 0.00226 (34229) covalent geometry : angle 0.56259 (46415) ********************** 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 265 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 199 time to evaluate : 3.767 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.3144 (pt) cc_final: 0.2670 (tp) REVERT: A 377 MET cc_start: 0.5455 (ttm) cc_final: 0.4603 (tmm) REVERT: A 430 MET cc_start: 0.7946 (ppp) cc_final: 0.7179 (ppp) REVERT: B 42 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7689 (mtmt) REVERT: B 74 ILE cc_start: 0.8455 (mm) cc_final: 0.7951 (mm) REVERT: D 80 LEU cc_start: 0.8746 (tt) cc_final: 0.8450 (mt) REVERT: D 528 MET cc_start: 0.8618 (mmm) cc_final: 0.8279 (mmm) REVERT: E 430 MET cc_start: 0.6506 (tmm) cc_final: 0.5718 (mtm) REVERT: E 473 LEU cc_start: 0.8032 (tp) cc_final: 0.7645 (mp) REVERT: E 748 ARG cc_start: 0.7240 (tpm170) cc_final: 0.6901 (tpm170) REVERT: F 143 MET cc_start: 0.5074 (OUTLIER) cc_final: 0.4579 (ppp) REVERT: C 53 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8226 (mt) outliers start: 66 outliers final: 57 residues processed: 255 average time/residue: 0.3999 time to fit residues: 180.6170 Evaluate side-chains 249 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 3.753 ------------------------------------------------------------------------------- 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 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 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 299 VAL Chi-restraints excluded: chain D residue 362 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 622 SER Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 261 ILE 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 762 THR 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 458 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 612 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 77 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 405 optimal weight: 4.9990 chunk 400 optimal weight: 0.9990 chunk 292 optimal weight: 20.0000 chunk 271 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 165 optimal weight: 0.2980 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.092695 restraints weight = 73453.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.090897 restraints weight = 55994.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091631 restraints weight = 45293.433| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 34229 Z= 0.189 Angle : 0.614 11.463 46415 Z= 0.308 Chirality : 0.044 0.317 5370 Planarity : 0.005 0.060 5976 Dihedral : 8.326 86.549 5037 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.30 % Favored : 93.30 % Rotamer: Outliers : 1.78 % Allowed : 15.90 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.13), residues: 4299 helix: 1.59 (0.13), residues: 1766 sheet: -0.10 (0.24), residues: 480 loop : -0.80 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 515 HIS 0.037 0.001 HIS C 91 PHE 0.020 0.001 PHE E 754 TYR 0.017 0.001 TYR D 768 ARG 0.008 0.000 ARG E 689 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 1285) hydrogen bonds : angle 4.11437 ( 3678) covalent geometry : bond 0.00454 (34229) covalent geometry : angle 0.61361 (46415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9062.84 seconds wall clock time: 159 minutes 27.74 seconds (9567.74 seconds total)