Starting phenix.real_space_refine on Thu Aug 8 12:53:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asl_43818/08_2024/9asl_43818.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asl_43818/08_2024/9asl_43818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asl_43818/08_2024/9asl_43818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asl_43818/08_2024/9asl_43818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asl_43818/08_2024/9asl_43818.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asl_43818/08_2024/9asl_43818.cif" } resolution = 3.5 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= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 14828 2.51 5 N 3956 2.21 5 O 4196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 736": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 593": "OE1" <-> "OE2" Residue "C GLU 736": "OE1" <-> "OE2" Residue "C GLU 872": "OE1" <-> "OE2" Residue "C GLU 874": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 685": "OE1" <-> "OE2" Residue "D GLU 736": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23128 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 11.88, per 1000 atoms: 0.51 Number of scatterers: 23128 At special positions: 0 Unit cell: (129.72, 138.92, 140.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 4196 8.00 N 3956 7.00 C 14828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.90 Conformation dependent library (CDL) restraints added in 4.2 seconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5568 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 23 sheets defined 56.8% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 93 through 102 removed outlier: 3.527A pdb=" N ALA A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.707A pdb=" N GLY A 120 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 removed outlier: 4.179A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.903A pdb=" N GLY A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 4.105A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.685A pdb=" N LEU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 325 through 337 removed outlier: 4.031A pdb=" N LEU A 329 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 365 removed outlier: 3.659A pdb=" N CYS A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.528A pdb=" N GLU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.867A pdb=" N LYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 411 Processing helix chain 'A' and resid 421 through 435 removed outlier: 4.008A pdb=" N ASP A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.968A pdb=" N GLN A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 removed outlier: 4.248A pdb=" N LYS A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 540 removed outlier: 3.500A pdb=" N ILE A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.850A pdb=" N MET A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.563A pdb=" N VAL A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TRP A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 592 " --> pdb=" O TRP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 624 through 636 removed outlier: 3.632A pdb=" N LEU A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 647 through 653 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 677 through 687 removed outlier: 3.914A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 685 " --> pdb=" O LYS A 681 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 729 removed outlier: 3.511A pdb=" N ASP A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 744 through 769 removed outlier: 4.122A pdb=" N SER A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 779 Processing helix chain 'A' and resid 780 through 788 removed outlier: 3.562A pdb=" N PHE A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 799 removed outlier: 4.329A pdb=" N ASP A 795 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 797 " --> pdb=" O CYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 827 through 835 removed outlier: 4.220A pdb=" N VAL A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 890 removed outlier: 3.510A pdb=" N VAL A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.534A pdb=" N ALA B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.816A pdb=" N GLY B 120 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 136 removed outlier: 4.274A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.860A pdb=" N GLY B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 removed outlier: 3.634A pdb=" N LEU B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.904A pdb=" N LEU B 329 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 335 " --> pdb=" O TYR B 331 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 364 removed outlier: 4.073A pdb=" N ASN B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.532A pdb=" N LEU B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.894A pdb=" N LYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 Processing helix chain 'B' and resid 421 through 435 removed outlier: 4.046A pdb=" N ASP B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 470 through 476 removed outlier: 3.961A pdb=" N GLN B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 removed outlier: 4.221A pdb=" N LYS B 503 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 540 removed outlier: 4.021A pdb=" N ARG B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'B' and resid 557 through 563 removed outlier: 3.797A pdb=" N MET B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 removed outlier: 3.823A pdb=" N VAL B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 592 " --> pdb=" O TRP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 624 through 641 removed outlier: 3.610A pdb=" N LEU B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 641 " --> pdb=" O ARG B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 653 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 677 through 687 removed outlier: 3.903A pdb=" N VAL B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 684 " --> pdb=" O MET B 680 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 729 removed outlier: 3.750A pdb=" N ASP B 727 " --> pdb=" O LEU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 744 through 769 removed outlier: 3.505A pdb=" N GLN B 749 " --> pdb=" O ARG B 745 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL B 764 " --> pdb=" O GLY B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 778 Processing helix chain 'B' and resid 780 through 788 removed outlier: 3.515A pdb=" N PHE B 787 " --> pdb=" O LYS B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 799 removed outlier: 4.288A pdb=" N ASP B 795 " --> pdb=" O GLU B 792 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 797 " --> pdb=" O CYS B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 827 through 835 removed outlier: 4.218A pdb=" N VAL B 831 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 832 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 890 removed outlier: 3.559A pdb=" N VAL B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 888 " --> pdb=" O ARG B 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.542A pdb=" N ALA C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.695A pdb=" N GLY C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 136 removed outlier: 4.296A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 162 Processing helix chain 'C' and resid 191 through 204 removed outlier: 3.882A pdb=" N GLY C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 245 removed outlier: 3.694A pdb=" N LEU C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.923A pdb=" N LEU C 329 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 365 removed outlier: 3.553A pdb=" N CYS C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.516A pdb=" N GLU C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 3.815A pdb=" N LYS C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 411 Processing helix chain 'C' and resid 421 through 435 removed outlier: 4.008A pdb=" N ASP C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 470 through 479 removed outlier: 3.990A pdb=" N GLN C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 510 removed outlier: 4.245A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 540 removed outlier: 4.024A pdb=" N ARG C 533 " --> pdb=" O GLY C 529 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 538 " --> pdb=" O ALA C 534 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 554 Processing helix chain 'C' and resid 557 through 563 removed outlier: 3.854A pdb=" N MET C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 592 removed outlier: 3.587A pdb=" N VAL C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TRP C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 592 " --> pdb=" O TRP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 Processing helix chain 'C' and resid 624 through 636 removed outlier: 3.643A pdb=" N LEU C 629 " --> pdb=" O PRO C 625 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 639 No H-bonds generated for 'chain 'C' and resid 637 through 639' Processing helix chain 'C' and resid 647 through 653 Processing helix chain 'C' and resid 665 through 676 Processing helix chain 'C' and resid 677 through 687 removed outlier: 3.865A pdb=" N VAL C 683 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 684 " --> pdb=" O MET C 680 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 685 " --> pdb=" O LYS C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 729 removed outlier: 3.501A pdb=" N ASP C 727 " --> pdb=" O LEU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 Processing helix chain 'C' and resid 744 through 769 removed outlier: 4.112A pdb=" N SER C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 757 " --> pdb=" O GLN C 753 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 779 Processing helix chain 'C' and resid 780 through 788 removed outlier: 3.626A pdb=" N PHE C 787 " --> pdb=" O LYS C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 799 removed outlier: 4.306A pdb=" N ASP C 795 " --> pdb=" O GLU C 792 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 797 " --> pdb=" O CYS C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 812 Processing helix chain 'C' and resid 817 through 822 Processing helix chain 'C' and resid 827 through 835 removed outlier: 4.202A pdb=" N VAL C 831 " --> pdb=" O VAL C 827 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 832 " --> pdb=" O GLU C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 890 removed outlier: 3.523A pdb=" N VAL C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 887 " --> pdb=" O ALA C 883 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN C 888 " --> pdb=" O ARG C 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 93 through 102 removed outlier: 3.502A pdb=" N ALA D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.757A pdb=" N GLY D 120 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 136 removed outlier: 4.296A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 162 Processing helix chain 'D' and resid 191 through 204 removed outlier: 3.790A pdb=" N GLY D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 245 removed outlier: 3.635A pdb=" N LEU D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.936A pdb=" N LEU D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS D 335 " --> pdb=" O TYR D 331 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 365 removed outlier: 4.056A pdb=" N ASN D 363 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 removed outlier: 3.540A pdb=" N GLU D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.903A pdb=" N LYS D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 421 through 435 removed outlier: 4.052A pdb=" N ASP D 426 " --> pdb=" O PHE D 422 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 449 Processing helix chain 'D' and resid 470 through 478 removed outlier: 3.882A pdb=" N GLN D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 478 " --> pdb=" O TYR D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 510 removed outlier: 4.243A pdb=" N LYS D 503 " --> pdb=" O SER D 499 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 506 " --> pdb=" O SER D 502 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 507 " --> pdb=" O LYS D 503 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 540 removed outlier: 4.027A pdb=" N ARG D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA D 534 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 538 " --> pdb=" O ALA D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 Processing helix chain 'D' and resid 557 through 563 removed outlier: 3.827A pdb=" N MET D 563 " --> pdb=" O LEU D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 592 removed outlier: 3.830A pdb=" N VAL D 586 " --> pdb=" O ILE D 582 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 592 " --> pdb=" O TRP D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 622 Processing helix chain 'D' and resid 624 through 636 removed outlier: 3.606A pdb=" N LEU D 629 " --> pdb=" O PRO D 625 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 653 Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 677 through 687 removed outlier: 3.892A pdb=" N VAL D 683 " --> pdb=" O SER D 679 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 684 " --> pdb=" O MET D 680 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 729 removed outlier: 3.632A pdb=" N ASP D 727 " --> pdb=" O LEU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 744 through 769 removed outlier: 4.032A pdb=" N SER D 754 " --> pdb=" O SER D 750 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 757 " --> pdb=" O GLN D 753 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL D 764 " --> pdb=" O GLY D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 778 Processing helix chain 'D' and resid 780 through 788 removed outlier: 3.512A pdb=" N PHE D 787 " --> pdb=" O LYS D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 799 removed outlier: 4.301A pdb=" N ASP D 795 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 797 " --> pdb=" O CYS D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 812 Processing helix chain 'D' and resid 817 through 822 Processing helix chain 'D' and resid 827 through 835 removed outlier: 4.223A pdb=" N VAL D 831 " --> pdb=" O VAL D 827 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 832 " --> pdb=" O GLU D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 890 removed outlier: 3.568A pdb=" N VAL D 880 " --> pdb=" O ALA D 876 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN D 888 " --> pdb=" O ARG D 884 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 4.111A pdb=" N VAL A 112 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 283 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 7.384A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS A 139 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 212 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 264 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 311 removed outlier: 4.028A pdb=" N ARG A 311 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 293 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU A 494 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 295 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 440 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA5, first strand: chain 'A' and resid 595 through 598 removed outlier: 3.507A pdb=" N HIS A 610 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 608 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AA7, first strand: chain 'B' and resid 264 through 265 removed outlier: 7.224A pdb=" N TYR B 113 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B 283 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 168 through 171 removed outlier: 5.689A pdb=" N LYS B 139 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET B 212 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 309 through 311 removed outlier: 4.039A pdb=" N ARG B 311 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 457 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 341 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 440 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 442 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 463 through 464 Processing sheet with id=AB2, first strand: chain 'B' and resid 595 through 597 removed outlier: 3.607A pdb=" N HIS B 610 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 862 through 863 Processing sheet with id=AB4, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.950A pdb=" N TYR C 283 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 168 through 171 removed outlier: 6.500A pdb=" N ASP C 169 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR C 190 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR C 171 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA C 140 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N CYS C 189 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 142 " --> pdb=" O CYS C 189 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LYS C 139 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET C 212 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 309 through 311 removed outlier: 4.026A pdb=" N ARG C 311 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS C 297 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 457 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 440 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 463 through 464 Processing sheet with id=AB8, first strand: chain 'C' and resid 595 through 598 removed outlier: 3.507A pdb=" N HIS C 610 " --> pdb=" O GLN C 596 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 608 " --> pdb=" O THR C 598 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 862 through 863 Processing sheet with id=AC1, first strand: chain 'D' and resid 168 through 171 removed outlier: 5.684A pdb=" N LYS D 139 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET D 212 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET D 264 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR D 283 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 309 through 311 removed outlier: 4.037A pdb=" N ARG D 311 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL D 457 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU D 341 " --> pdb=" O ILE D 458 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 440 " --> pdb=" O VAL D 340 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 463 through 464 Processing sheet with id=AC4, first strand: chain 'D' and resid 595 through 597 removed outlier: 3.607A pdb=" N HIS D 610 " --> pdb=" O GLN D 596 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 862 through 863 1034 hydrogen bonds defined for protein. 2937 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: 8.28 Time building geometry restraints manager: 9.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7509 1.34 - 1.46: 5043 1.46 - 1.58: 10740 1.58 - 1.70: 0 1.70 - 1.81: 236 Bond restraints: 23528 Sorted by residual: bond pdb=" CA VAL D 409 " pdb=" CB VAL D 409 " ideal model delta sigma weight residual 1.539 1.528 0.011 5.40e-03 3.43e+04 4.46e+00 bond pdb=" C LEU A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 1.332 1.350 -0.019 1.26e-02 6.30e+03 2.19e+00 bond pdb=" C LEU B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.34e-02 5.57e+03 2.07e+00 bond pdb=" C LEU D 76 " pdb=" N PRO D 77 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.34e-02 5.57e+03 2.01e+00 bond pdb=" C LEU C 76 " pdb=" N PRO C 77 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.33e-02 5.65e+03 2.01e+00 ... (remaining 23523 not shown) Histogram of bond angle deviations from ideal: 97.44 - 104.76: 282 104.76 - 112.08: 11948 112.08 - 119.39: 8071 119.39 - 126.71: 11210 126.71 - 134.03: 313 Bond angle restraints: 31824 Sorted by residual: angle pdb=" N VAL A 687 " pdb=" CA VAL A 687 " pdb=" C VAL A 687 " ideal model delta sigma weight residual 113.10 110.03 3.07 9.70e-01 1.06e+00 1.00e+01 angle pdb=" N GLN D 805 " pdb=" CA GLN D 805 " pdb=" C GLN D 805 " ideal model delta sigma weight residual 114.04 110.14 3.90 1.24e+00 6.50e-01 9.88e+00 angle pdb=" N GLU D 126 " pdb=" CA GLU D 126 " pdb=" CB GLU D 126 " ideal model delta sigma weight residual 110.16 114.77 -4.61 1.48e+00 4.57e-01 9.71e+00 angle pdb=" N GLU B 126 " pdb=" CA GLU B 126 " pdb=" CB GLU B 126 " ideal model delta sigma weight residual 110.16 114.72 -4.56 1.48e+00 4.57e-01 9.51e+00 angle pdb=" CA GLU B 736 " pdb=" CB GLU B 736 " pdb=" CG GLU B 736 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.48e+00 ... (remaining 31819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 11605 17.55 - 35.10: 1929 35.10 - 52.64: 478 52.64 - 70.19: 98 70.19 - 87.74: 42 Dihedral angle restraints: 14152 sinusoidal: 5580 harmonic: 8572 Sorted by residual: dihedral pdb=" CA ASP D 304 " pdb=" CB ASP D 304 " pdb=" CG ASP D 304 " pdb=" OD1 ASP D 304 " ideal model delta sinusoidal sigma weight residual -30.00 -88.05 58.05 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA HIS B 180 " pdb=" C HIS B 180 " pdb=" N PHE B 181 " pdb=" CA PHE B 181 " ideal model delta harmonic sigma weight residual -180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CG ARG D 533 " pdb=" CD ARG D 533 " pdb=" NE ARG D 533 " pdb=" CZ ARG D 533 " ideal model delta sinusoidal sigma weight residual -90.00 -134.95 44.95 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 14149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2552 0.038 - 0.076: 947 0.076 - 0.113: 193 0.113 - 0.151: 58 0.151 - 0.189: 2 Chirality restraints: 3752 Sorted by residual: chirality pdb=" CA GLU B 126 " pdb=" N GLU B 126 " pdb=" C GLU B 126 " pdb=" CB GLU B 126 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA GLU D 126 " pdb=" N GLU D 126 " pdb=" C GLU D 126 " pdb=" CB GLU D 126 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CG LEU B 619 " pdb=" CB LEU B 619 " pdb=" CD1 LEU B 619 " pdb=" CD2 LEU B 619 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 3749 not shown) Planarity restraints: 3980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 344 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 345 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 344 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO B 345 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO B 345 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 345 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 344 " -0.071 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO D 345 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO D 345 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 345 " -0.057 5.00e-02 4.00e+02 ... (remaining 3977 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 671 2.70 - 3.25: 23644 3.25 - 3.80: 36484 3.80 - 4.35: 46676 4.35 - 4.90: 76177 Nonbonded interactions: 183652 Sorted by model distance: nonbonded pdb=" NZ LYS C 109 " pdb=" OE1 GLU C 281 " model vdw 2.155 3.120 nonbonded pdb=" O HIS B 180 " pdb=" OG SER B 183 " model vdw 2.160 3.040 nonbonded pdb=" O LYS A 83 " pdb=" OG SER A 86 " model vdw 2.167 3.040 nonbonded pdb=" O HIS D 180 " pdb=" OG SER D 183 " model vdw 2.190 3.040 nonbonded pdb=" OG SER A 114 " pdb=" O ALA A 266 " model vdw 2.207 3.040 ... (remaining 183647 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 29.350 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 59.680 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23528 Z= 0.219 Angle : 0.660 9.260 31824 Z= 0.350 Chirality : 0.041 0.189 3752 Planarity : 0.005 0.115 3980 Dihedral : 18.706 87.741 8584 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.48 % Allowed : 35.90 % Favored : 63.62 % 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: -1.52 (0.15), residues: 2892 helix: -0.75 (0.13), residues: 1468 sheet: -0.13 (0.38), residues: 204 loop : -1.35 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 349 HIS 0.016 0.001 HIS A 85 PHE 0.018 0.001 PHE B 343 TYR 0.026 0.002 TYR B 228 ARG 0.009 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 525 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8614 (mp) cc_final: 0.8397 (mp) REVERT: A 713 MET cc_start: 0.8336 (tpt) cc_final: 0.7679 (tpt) REVERT: B 94 GLU cc_start: 0.7609 (pm20) cc_final: 0.6863 (tm-30) REVERT: B 634 ASP cc_start: 0.7879 (t0) cc_final: 0.7471 (t0) REVERT: B 639 MET cc_start: 0.6455 (mmt) cc_final: 0.5721 (mmt) REVERT: B 774 MET cc_start: 0.6779 (ptp) cc_final: 0.6548 (ptp) REVERT: D 92 MET cc_start: 0.5388 (tpp) cc_final: 0.4686 (tpp) REVERT: D 94 GLU cc_start: 0.7572 (pm20) cc_final: 0.6955 (tm-30) REVERT: D 634 ASP cc_start: 0.7867 (t0) cc_final: 0.7494 (t0) outliers start: 12 outliers final: 6 residues processed: 530 average time/residue: 0.3532 time to fit residues: 286.8657 Evaluate side-chains 363 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 357 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 142 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 443 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 0.0370 chunk 76 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 172 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 overall best weight: 1.3060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 HIS A 498 ASN A 646 ASN A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN C 416 HIS C 498 ASN C 646 ASN C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 ASN ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23528 Z= 0.317 Angle : 0.679 8.349 31824 Z= 0.347 Chirality : 0.043 0.173 3752 Planarity : 0.005 0.075 3980 Dihedral : 4.786 55.653 3169 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.09 % Rotamer: Outliers : 5.47 % Allowed : 33.51 % Favored : 61.02 % 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: -1.22 (0.15), residues: 2892 helix: -0.25 (0.13), residues: 1564 sheet: -0.05 (0.36), residues: 208 loop : -1.67 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 411 HIS 0.009 0.001 HIS A 85 PHE 0.015 0.002 PHE B 658 TYR 0.023 0.002 TYR B 239 ARG 0.007 0.001 ARG B 823 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 381 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7411 (mmmt) cc_final: 0.7124 (tppt) REVERT: A 92 MET cc_start: 0.7337 (ttm) cc_final: 0.6880 (ttp) REVERT: A 307 MET cc_start: 0.6298 (mmt) cc_final: 0.5987 (mpp) REVERT: A 713 MET cc_start: 0.8165 (tpt) cc_final: 0.7452 (tpt) REVERT: B 92 MET cc_start: 0.5945 (tpp) cc_final: 0.5501 (tpp) REVERT: B 94 GLU cc_start: 0.7676 (pm20) cc_final: 0.7029 (tm-30) REVERT: B 216 ASP cc_start: 0.7994 (m-30) cc_final: 0.7678 (m-30) REVERT: B 634 ASP cc_start: 0.7768 (t0) cc_final: 0.7535 (t0) REVERT: B 639 MET cc_start: 0.6476 (mmt) cc_final: 0.5283 (mmt) REVERT: B 878 LEU cc_start: 0.7721 (mt) cc_final: 0.7461 (mt) REVERT: C 91 LYS cc_start: 0.7344 (mmmt) cc_final: 0.7035 (tppt) REVERT: C 92 MET cc_start: 0.6945 (ttp) cc_final: 0.6535 (ttm) REVERT: C 307 MET cc_start: 0.6299 (mmt) cc_final: 0.5975 (mpp) REVERT: D 92 MET cc_start: 0.5809 (tpp) cc_final: 0.4861 (tpp) REVERT: D 94 GLU cc_start: 0.7649 (pm20) cc_final: 0.7053 (tm-30) REVERT: D 144 LEU cc_start: 0.8489 (mm) cc_final: 0.8286 (mt) REVERT: D 634 ASP cc_start: 0.7791 (t0) cc_final: 0.7510 (t0) REVERT: D 878 LEU cc_start: 0.7847 (mt) cc_final: 0.7493 (mt) outliers start: 137 outliers final: 59 residues processed: 478 average time/residue: 0.3039 time to fit residues: 237.0858 Evaluate side-chains 399 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 340 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 PHE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 859 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 0.0170 chunk 223 optimal weight: 0.0010 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 290 optimal weight: 0.9980 chunk 239 optimal weight: 0.7980 chunk 267 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 overall best weight: 0.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23528 Z= 0.190 Angle : 0.588 13.357 31824 Z= 0.296 Chirality : 0.041 0.251 3752 Planarity : 0.004 0.065 3980 Dihedral : 4.530 57.901 3165 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.03 % Allowed : 33.31 % Favored : 61.66 % 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: -0.81 (0.15), residues: 2892 helix: 0.08 (0.13), residues: 1580 sheet: 0.07 (0.35), residues: 208 loop : -1.47 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 411 HIS 0.007 0.001 HIS A 325 PHE 0.015 0.002 PHE C 787 TYR 0.018 0.001 TYR B 239 ARG 0.007 0.000 ARG C 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 405 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7006 (mtpt) cc_final: 0.6497 (ttpt) REVERT: A 307 MET cc_start: 0.6125 (mmt) cc_final: 0.5816 (mpp) REVERT: A 713 MET cc_start: 0.8002 (tpt) cc_final: 0.7525 (tpt) REVERT: B 351 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5834 (mt-10) REVERT: B 366 HIS cc_start: 0.3510 (OUTLIER) cc_final: 0.2949 (m-70) REVERT: B 668 ARG cc_start: 0.6935 (mtp85) cc_final: 0.6664 (mmm-85) REVERT: B 680 MET cc_start: 0.7720 (mtm) cc_final: 0.7203 (mtm) REVERT: B 878 LEU cc_start: 0.7869 (mt) cc_final: 0.7555 (mt) REVERT: C 307 MET cc_start: 0.6203 (mmt) cc_final: 0.5861 (mpp) REVERT: C 366 HIS cc_start: 0.3444 (OUTLIER) cc_final: 0.2859 (m-70) REVERT: C 713 MET cc_start: 0.8484 (tpt) cc_final: 0.7683 (tpt) REVERT: C 878 LEU cc_start: 0.7708 (mt) cc_final: 0.7253 (mt) REVERT: D 92 MET cc_start: 0.5868 (tpp) cc_final: 0.5616 (tpp) REVERT: D 94 GLU cc_start: 0.7498 (pm20) cc_final: 0.6959 (tm-30) REVERT: D 233 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8441 (tp) REVERT: D 634 ASP cc_start: 0.7794 (t0) cc_final: 0.7452 (t0) REVERT: D 878 LEU cc_start: 0.7948 (mt) cc_final: 0.7576 (mt) outliers start: 126 outliers final: 59 residues processed: 500 average time/residue: 0.3028 time to fit residues: 245.0272 Evaluate side-chains 409 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 346 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 0.3980 chunk 180 optimal weight: 0.7980 chunk 270 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 260 GLN ** D 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23528 Z= 0.233 Angle : 0.602 13.209 31824 Z= 0.300 Chirality : 0.042 0.326 3752 Planarity : 0.004 0.061 3980 Dihedral : 4.341 54.557 3162 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.75 % Allowed : 33.99 % Favored : 61.26 % 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: -0.65 (0.15), residues: 2892 helix: 0.21 (0.13), residues: 1576 sheet: -0.11 (0.31), residues: 256 loop : -1.38 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 411 HIS 0.007 0.001 HIS A 325 PHE 0.020 0.002 PHE C 670 TYR 0.017 0.001 TYR A 171 ARG 0.004 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 384 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7586 (mmmt) cc_final: 0.7377 (tppt) REVERT: A 121 LYS cc_start: 0.7055 (mtpt) cc_final: 0.6422 (ttpt) REVERT: A 307 MET cc_start: 0.6044 (mmt) cc_final: 0.5744 (mpp) REVERT: A 366 HIS cc_start: 0.3430 (OUTLIER) cc_final: 0.2968 (m-70) REVERT: A 624 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7818 (p) REVERT: A 680 MET cc_start: 0.7380 (mtm) cc_final: 0.7009 (mtm) REVERT: A 862 ILE cc_start: 0.5761 (OUTLIER) cc_final: 0.5505 (tt) REVERT: A 878 LEU cc_start: 0.7569 (mt) cc_final: 0.7282 (mt) REVERT: B 81 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8346 (pp) REVERT: B 142 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7886 (t80) REVERT: B 351 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5833 (mt-10) REVERT: B 878 LEU cc_start: 0.7946 (mt) cc_final: 0.7468 (mt) REVERT: C 91 LYS cc_start: 0.7207 (tppt) cc_final: 0.6547 (tmtt) REVERT: C 307 MET cc_start: 0.6094 (mmt) cc_final: 0.5769 (mpp) REVERT: C 366 HIS cc_start: 0.3631 (OUTLIER) cc_final: 0.3105 (m-70) REVERT: C 624 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.7791 (p) REVERT: C 878 LEU cc_start: 0.7703 (mt) cc_final: 0.7366 (mt) REVERT: D 92 MET cc_start: 0.6553 (tpp) cc_final: 0.5891 (tpp) REVERT: D 233 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8393 (tp) REVERT: D 366 HIS cc_start: 0.3577 (OUTLIER) cc_final: 0.2937 (m-70) REVERT: D 634 ASP cc_start: 0.7771 (t0) cc_final: 0.7398 (t0) REVERT: D 668 ARG cc_start: 0.7088 (mtp85) cc_final: 0.6780 (mtt-85) REVERT: D 878 LEU cc_start: 0.8070 (mt) cc_final: 0.7550 (mt) outliers start: 119 outliers final: 71 residues processed: 475 average time/residue: 0.3061 time to fit residues: 236.0453 Evaluate side-chains 423 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 342 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 744 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN A 325 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 HIS ** D 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 ASN ** D 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 23528 Z= 0.377 Angle : 0.703 15.443 31824 Z= 0.350 Chirality : 0.046 0.409 3752 Planarity : 0.005 0.064 3980 Dihedral : 4.551 22.166 3160 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.84 % Favored : 95.06 % Rotamer: Outliers : 6.19 % Allowed : 32.75 % Favored : 61.06 % 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: -0.84 (0.15), residues: 2892 helix: 0.06 (0.13), residues: 1576 sheet: -0.71 (0.29), residues: 300 loop : -1.33 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 673 HIS 0.007 0.001 HIS C 325 PHE 0.019 0.003 PHE A 719 TYR 0.016 0.002 TYR A 228 ARG 0.006 0.001 ARG C 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 363 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7802 (mmmt) cc_final: 0.6729 (tmtt) REVERT: A 121 LYS cc_start: 0.7178 (mtpt) cc_final: 0.6581 (ttpt) REVERT: A 351 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6027 (mt-10) REVERT: A 366 HIS cc_start: 0.3849 (OUTLIER) cc_final: 0.3276 (m-70) REVERT: A 718 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7693 (ttt-90) REVERT: A 878 LEU cc_start: 0.7720 (mt) cc_final: 0.7415 (mt) REVERT: B 81 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8398 (pp) REVERT: B 92 MET cc_start: 0.6251 (tpp) cc_final: 0.5997 (tpp) REVERT: B 122 THR cc_start: 0.7952 (p) cc_final: 0.7706 (t) REVERT: B 142 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8137 (t80) REVERT: B 351 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5915 (mt-10) REVERT: B 366 HIS cc_start: 0.3975 (OUTLIER) cc_final: 0.3499 (m-70) REVERT: B 422 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7972 (t80) REVERT: B 423 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7314 (mp0) REVERT: B 667 TYR cc_start: 0.7210 (t80) cc_final: 0.6908 (t80) REVERT: B 680 MET cc_start: 0.8074 (mtm) cc_final: 0.7849 (mpp) REVERT: B 718 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7663 (ttt-90) REVERT: B 878 LEU cc_start: 0.7843 (mt) cc_final: 0.7523 (mt) REVERT: C 81 LEU cc_start: 0.8825 (pp) cc_final: 0.8394 (pp) REVERT: C 351 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6227 (mt-10) REVERT: C 366 HIS cc_start: 0.4023 (OUTLIER) cc_final: 0.3561 (m-70) REVERT: C 713 MET cc_start: 0.8557 (tpt) cc_final: 0.7869 (tpt) REVERT: C 718 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7752 (ttt-90) REVERT: C 862 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6677 (tp) REVERT: C 878 LEU cc_start: 0.7823 (mt) cc_final: 0.7495 (mt) REVERT: D 92 MET cc_start: 0.6913 (tpp) cc_final: 0.5967 (tpp) REVERT: D 142 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8176 (t80) REVERT: D 233 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8517 (tp) REVERT: D 366 HIS cc_start: 0.3799 (OUTLIER) cc_final: 0.3369 (m-70) REVERT: D 634 ASP cc_start: 0.7715 (t0) cc_final: 0.7284 (t0) REVERT: D 718 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7675 (ttt-90) REVERT: D 878 LEU cc_start: 0.7940 (mt) cc_final: 0.7543 (mt) outliers start: 155 outliers final: 92 residues processed: 488 average time/residue: 0.3122 time to fit residues: 244.7688 Evaluate side-chains 440 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 331 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 56 optimal weight: 0.0770 chunk 167 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 286 optimal weight: 0.5980 chunk 237 optimal weight: 0.4980 chunk 132 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN D 85 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23528 Z= 0.182 Angle : 0.588 10.313 31824 Z= 0.295 Chirality : 0.042 0.328 3752 Planarity : 0.004 0.061 3980 Dihedral : 4.320 21.001 3160 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 4.39 % Allowed : 34.70 % Favored : 60.90 % 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: -0.71 (0.15), residues: 2892 helix: 0.18 (0.13), residues: 1608 sheet: -0.36 (0.30), residues: 280 loop : -1.45 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 863 HIS 0.008 0.001 HIS B 716 PHE 0.012 0.001 PHE C 343 TYR 0.015 0.001 TYR B 171 ARG 0.005 0.000 ARG C 798 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 368 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7839 (mmmt) cc_final: 0.6848 (tmtt) REVERT: A 92 MET cc_start: 0.7596 (ttm) cc_final: 0.7323 (ttp) REVERT: A 121 LYS cc_start: 0.7037 (mtpt) cc_final: 0.6519 (ttpt) REVERT: A 351 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5927 (mt-10) REVERT: A 366 HIS cc_start: 0.3651 (OUTLIER) cc_final: 0.3026 (m-70) REVERT: A 878 LEU cc_start: 0.7682 (mt) cc_final: 0.7402 (mt) REVERT: B 142 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8123 (t80) REVERT: B 166 ILE cc_start: 0.7985 (mp) cc_final: 0.7769 (pt) REVERT: B 351 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5587 (mt-10) REVERT: B 366 HIS cc_start: 0.3805 (OUTLIER) cc_final: 0.3337 (m-70) REVERT: B 422 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7743 (t80) REVERT: B 423 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7170 (mp0) REVERT: B 718 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7542 (ttt-90) REVERT: B 878 LEU cc_start: 0.7805 (mt) cc_final: 0.7503 (mt) REVERT: C 91 LYS cc_start: 0.7189 (tppt) cc_final: 0.6314 (tmtt) REVERT: C 366 HIS cc_start: 0.3908 (OUTLIER) cc_final: 0.3407 (m-70) REVERT: C 639 MET cc_start: 0.6897 (ppp) cc_final: 0.6414 (ptm) REVERT: C 718 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7729 (ttt-90) REVERT: C 878 LEU cc_start: 0.7809 (mt) cc_final: 0.7444 (mt) REVERT: D 92 MET cc_start: 0.6866 (tpp) cc_final: 0.5955 (tpp) REVERT: D 142 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8037 (t80) REVERT: D 166 ILE cc_start: 0.8006 (mp) cc_final: 0.7794 (pt) REVERT: D 207 MET cc_start: 0.8417 (mmm) cc_final: 0.7937 (mmm) REVERT: D 233 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8421 (tp) REVERT: D 366 HIS cc_start: 0.3896 (OUTLIER) cc_final: 0.3458 (m-70) REVERT: D 634 ASP cc_start: 0.7711 (t0) cc_final: 0.7215 (t0) REVERT: D 680 MET cc_start: 0.7951 (mtm) cc_final: 0.7401 (mtm) REVERT: D 718 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7584 (ttt-90) REVERT: D 878 LEU cc_start: 0.7928 (mt) cc_final: 0.7547 (mt) outliers start: 110 outliers final: 62 residues processed: 455 average time/residue: 0.3009 time to fit residues: 222.2867 Evaluate side-chains 411 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 336 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 361 PHE Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 737 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 178 optimal weight: 0.0870 chunk 173 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS ** D 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23528 Z= 0.225 Angle : 0.606 12.332 31824 Z= 0.300 Chirality : 0.042 0.364 3752 Planarity : 0.004 0.071 3980 Dihedral : 4.244 17.645 3160 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 4.59 % Allowed : 34.66 % Favored : 60.74 % 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: -0.72 (0.15), residues: 2892 helix: 0.18 (0.13), residues: 1620 sheet: -0.55 (0.27), residues: 340 loop : -1.45 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 74 HIS 0.012 0.001 HIS D 716 PHE 0.012 0.001 PHE C 343 TYR 0.018 0.001 TYR D 171 ARG 0.018 0.000 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 345 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7019 (mtpt) cc_final: 0.6470 (ttpt) REVERT: A 351 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5860 (mt-10) REVERT: A 366 HIS cc_start: 0.3691 (OUTLIER) cc_final: 0.3127 (m-70) REVERT: A 718 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7675 (ttt-90) REVERT: A 878 LEU cc_start: 0.7720 (mt) cc_final: 0.7381 (mt) REVERT: B 91 LYS cc_start: 0.7470 (tppt) cc_final: 0.7087 (tptp) REVERT: B 121 LYS cc_start: 0.6903 (mtpt) cc_final: 0.6405 (ttpt) REVERT: B 142 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8079 (t80) REVERT: B 351 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5623 (mt-10) REVERT: B 366 HIS cc_start: 0.4016 (OUTLIER) cc_final: 0.3543 (m-70) REVERT: B 422 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7665 (t80) REVERT: B 423 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7225 (mp0) REVERT: B 718 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7606 (ttt-90) REVERT: B 878 LEU cc_start: 0.7840 (mt) cc_final: 0.7509 (mt) REVERT: C 166 ILE cc_start: 0.8347 (mp) cc_final: 0.8031 (mp) REVERT: C 351 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6054 (mt-10) REVERT: C 366 HIS cc_start: 0.4011 (OUTLIER) cc_final: 0.3514 (m-70) REVERT: C 587 MET cc_start: 0.7818 (tpp) cc_final: 0.7508 (tpt) REVERT: C 639 MET cc_start: 0.6897 (ppp) cc_final: 0.6386 (ptm) REVERT: C 718 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7734 (ttt-90) REVERT: C 878 LEU cc_start: 0.7842 (mt) cc_final: 0.7471 (mt) REVERT: D 92 MET cc_start: 0.6924 (tpp) cc_final: 0.6023 (tpp) REVERT: D 142 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8054 (t80) REVERT: D 207 MET cc_start: 0.8447 (mmm) cc_final: 0.8032 (mmm) REVERT: D 233 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8472 (tp) REVERT: D 366 HIS cc_start: 0.3994 (OUTLIER) cc_final: 0.3564 (m-70) REVERT: D 634 ASP cc_start: 0.7667 (t0) cc_final: 0.7178 (t0) REVERT: D 680 MET cc_start: 0.8064 (mtm) cc_final: 0.7550 (mtm) REVERT: D 718 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7620 (ttt-90) REVERT: D 878 LEU cc_start: 0.7961 (mt) cc_final: 0.7556 (mt) outliers start: 115 outliers final: 76 residues processed: 437 average time/residue: 0.3105 time to fit residues: 218.3885 Evaluate side-chains 421 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 330 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 361 PHE Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 194 optimal weight: 0.0570 chunk 141 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 224 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23528 Z= 0.198 Angle : 0.592 11.565 31824 Z= 0.292 Chirality : 0.041 0.402 3752 Planarity : 0.004 0.057 3980 Dihedral : 4.169 16.106 3160 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.23 % Allowed : 34.82 % Favored : 60.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.15), residues: 2892 helix: 0.26 (0.13), residues: 1612 sheet: -0.42 (0.27), residues: 336 loop : -1.52 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 673 HIS 0.008 0.001 HIS D 716 PHE 0.010 0.001 PHE C 343 TYR 0.021 0.001 TYR A 667 ARG 0.011 0.000 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 339 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7787 (mmmt) cc_final: 0.6595 (tmtt) REVERT: A 121 LYS cc_start: 0.6944 (mtpt) cc_final: 0.6426 (ttpt) REVERT: A 233 LEU cc_start: 0.8546 (tt) cc_final: 0.8311 (tp) REVERT: A 351 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5914 (mt-10) REVERT: A 366 HIS cc_start: 0.3677 (OUTLIER) cc_final: 0.3102 (m-70) REVERT: A 417 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8320 (p90) REVERT: A 587 MET cc_start: 0.7799 (tpp) cc_final: 0.7444 (tpt) REVERT: A 718 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7739 (ttt-90) REVERT: A 878 LEU cc_start: 0.7719 (mt) cc_final: 0.7391 (mt) REVERT: B 142 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8079 (t80) REVERT: B 351 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5618 (mt-10) REVERT: B 366 HIS cc_start: 0.4048 (OUTLIER) cc_final: 0.3617 (m-70) REVERT: B 422 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7633 (t80) REVERT: B 423 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7239 (mp0) REVERT: B 718 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7585 (ttt-90) REVERT: B 878 LEU cc_start: 0.7833 (mt) cc_final: 0.7525 (mt) REVERT: C 166 ILE cc_start: 0.8354 (mp) cc_final: 0.8045 (mp) REVERT: C 351 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6109 (mt-10) REVERT: C 366 HIS cc_start: 0.3955 (OUTLIER) cc_final: 0.3504 (m-70) REVERT: C 587 MET cc_start: 0.7806 (tpp) cc_final: 0.7501 (tpt) REVERT: C 639 MET cc_start: 0.6869 (ppp) cc_final: 0.6449 (ptm) REVERT: C 718 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7684 (ttt-90) REVERT: C 878 LEU cc_start: 0.7817 (mt) cc_final: 0.7477 (mt) REVERT: D 92 MET cc_start: 0.6854 (tpp) cc_final: 0.5924 (tpp) REVERT: D 142 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8061 (t80) REVERT: D 233 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8478 (tp) REVERT: D 366 HIS cc_start: 0.4054 (OUTLIER) cc_final: 0.3646 (m-70) REVERT: D 634 ASP cc_start: 0.7673 (t0) cc_final: 0.7092 (t0) REVERT: D 680 MET cc_start: 0.8068 (mtm) cc_final: 0.7494 (mtm) REVERT: D 718 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7609 (ttt-90) REVERT: D 878 LEU cc_start: 0.7943 (mt) cc_final: 0.7549 (mt) outliers start: 106 outliers final: 74 residues processed: 424 average time/residue: 0.3025 time to fit residues: 208.6258 Evaluate side-chains 413 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 323 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 361 PHE Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.0030 chunk 273 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 265 optimal weight: 0.5980 chunk 160 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 GLN ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23528 Z= 0.240 Angle : 0.619 10.401 31824 Z= 0.305 Chirality : 0.043 0.450 3752 Planarity : 0.004 0.057 3980 Dihedral : 4.177 16.616 3160 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.51 % Allowed : 34.82 % Favored : 60.66 % 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: -0.59 (0.15), residues: 2892 helix: 0.29 (0.13), residues: 1628 sheet: -0.33 (0.28), residues: 320 loop : -1.48 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 673 HIS 0.007 0.001 HIS D 716 PHE 0.013 0.001 PHE C 343 TYR 0.016 0.001 TYR B 171 ARG 0.005 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 340 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7014 (mtpt) cc_final: 0.6486 (ttpt) REVERT: A 351 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.6029 (mt-10) REVERT: A 366 HIS cc_start: 0.3759 (OUTLIER) cc_final: 0.3205 (m-70) REVERT: A 417 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.8348 (p90) REVERT: A 718 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7802 (ttt-90) REVERT: A 878 LEU cc_start: 0.7724 (mt) cc_final: 0.7397 (mt) REVERT: B 91 LYS cc_start: 0.7436 (tppt) cc_final: 0.7054 (tptp) REVERT: B 142 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8097 (t80) REVERT: B 351 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5610 (mt-10) REVERT: B 366 HIS cc_start: 0.4101 (OUTLIER) cc_final: 0.3701 (m-70) REVERT: B 422 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7602 (t80) REVERT: B 423 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7275 (mp0) REVERT: B 718 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7576 (ttt-90) REVERT: B 878 LEU cc_start: 0.7859 (mt) cc_final: 0.7549 (mt) REVERT: C 351 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6217 (mt-10) REVERT: C 366 HIS cc_start: 0.4098 (OUTLIER) cc_final: 0.3671 (m-70) REVERT: C 587 MET cc_start: 0.7832 (tpp) cc_final: 0.7523 (tpt) REVERT: C 639 MET cc_start: 0.6859 (ppp) cc_final: 0.6589 (ppp) REVERT: C 718 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7704 (ttt-90) REVERT: C 878 LEU cc_start: 0.7862 (mt) cc_final: 0.7516 (mt) REVERT: D 92 MET cc_start: 0.6846 (tpp) cc_final: 0.5771 (tpp) REVERT: D 142 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8070 (t80) REVERT: D 233 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8573 (tp) REVERT: D 366 HIS cc_start: 0.4066 (OUTLIER) cc_final: 0.3729 (m-70) REVERT: D 477 MET cc_start: 0.6696 (tpt) cc_final: 0.6159 (tpt) REVERT: D 634 ASP cc_start: 0.7649 (t0) cc_final: 0.7243 (t0) REVERT: D 718 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7573 (ttt-90) REVERT: D 878 LEU cc_start: 0.7986 (mt) cc_final: 0.7579 (mt) outliers start: 113 outliers final: 83 residues processed: 431 average time/residue: 0.3154 time to fit residues: 219.9186 Evaluate side-chains 431 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 332 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 361 PHE Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.9980 chunk 281 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 133 optimal weight: 0.1980 chunk 195 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 chunk 271 optimal weight: 0.8980 chunk 234 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 143 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23528 Z= 0.202 Angle : 0.610 10.111 31824 Z= 0.300 Chirality : 0.042 0.416 3752 Planarity : 0.004 0.060 3980 Dihedral : 4.139 16.268 3160 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.11 % Allowed : 34.82 % Favored : 61.06 % 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: -0.51 (0.15), residues: 2892 helix: 0.36 (0.13), residues: 1620 sheet: -0.18 (0.29), residues: 316 loop : -1.48 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 673 HIS 0.007 0.001 HIS D 716 PHE 0.013 0.001 PHE C 343 TYR 0.021 0.001 TYR D 667 ARG 0.007 0.000 ARG D 873 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 346 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7044 (mtpt) cc_final: 0.6597 (ttpt) REVERT: A 351 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5889 (mt-10) REVERT: A 366 HIS cc_start: 0.3724 (OUTLIER) cc_final: 0.3191 (m-70) REVERT: A 718 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7731 (ttt-90) REVERT: A 878 LEU cc_start: 0.7706 (mt) cc_final: 0.7381 (mt) REVERT: B 91 LYS cc_start: 0.7501 (tppt) cc_final: 0.7032 (tptp) REVERT: B 142 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8057 (t80) REVERT: B 351 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.5605 (mt-10) REVERT: B 366 HIS cc_start: 0.4144 (OUTLIER) cc_final: 0.3765 (m-70) REVERT: B 422 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7636 (t80) REVERT: B 423 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7193 (mp0) REVERT: B 667 TYR cc_start: 0.7141 (t80) cc_final: 0.6923 (t80) REVERT: B 680 MET cc_start: 0.8078 (mpp) cc_final: 0.7750 (mpp) REVERT: B 718 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7597 (ttt-90) REVERT: B 878 LEU cc_start: 0.7848 (mt) cc_final: 0.7543 (mt) REVERT: C 91 LYS cc_start: 0.7262 (tppt) cc_final: 0.6126 (tmtt) REVERT: C 166 ILE cc_start: 0.8280 (mp) cc_final: 0.8005 (mp) REVERT: C 206 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7527 (ttpt) REVERT: C 351 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.6113 (mt-10) REVERT: C 366 HIS cc_start: 0.4126 (OUTLIER) cc_final: 0.3696 (m-70) REVERT: C 587 MET cc_start: 0.7822 (tpp) cc_final: 0.7518 (tpt) REVERT: C 639 MET cc_start: 0.6850 (ppp) cc_final: 0.6485 (ptm) REVERT: C 718 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7676 (ttt-90) REVERT: C 878 LEU cc_start: 0.7857 (mt) cc_final: 0.7518 (mt) REVERT: D 92 MET cc_start: 0.6653 (tpp) cc_final: 0.5593 (tpp) REVERT: D 142 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8064 (t80) REVERT: D 233 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8583 (tp) REVERT: D 366 HIS cc_start: 0.4037 (OUTLIER) cc_final: 0.3737 (m-70) REVERT: D 422 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7540 (t80) REVERT: D 634 ASP cc_start: 0.7672 (t0) cc_final: 0.7125 (t0) REVERT: D 718 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7800 (ttt-90) REVERT: D 878 LEU cc_start: 0.8017 (mt) cc_final: 0.7609 (mt) outliers start: 103 outliers final: 71 residues processed: 428 average time/residue: 0.3051 time to fit residues: 208.7577 Evaluate side-chains 417 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 329 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 361 PHE Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 7.9990 chunk 250 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 235 optimal weight: 0.0050 chunk 98 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 ASN B 85 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.193334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.146929 restraints weight = 37107.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.151460 restraints weight = 19154.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.154453 restraints weight = 13005.307| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23528 Z= 0.205 Angle : 0.614 12.162 31824 Z= 0.301 Chirality : 0.042 0.412 3752 Planarity : 0.004 0.061 3980 Dihedral : 4.113 16.567 3160 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.83 % Allowed : 34.94 % Favored : 61.22 % 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: -0.49 (0.15), residues: 2892 helix: 0.35 (0.13), residues: 1624 sheet: -0.13 (0.29), residues: 316 loop : -1.45 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 673 HIS 0.008 0.001 HIS B 325 PHE 0.013 0.001 PHE C 343 TYR 0.021 0.001 TYR D 667 ARG 0.005 0.000 ARG C 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5183.81 seconds wall clock time: 94 minutes 31.92 seconds (5671.92 seconds total)