Starting phenix.real_space_refine on Mon Mar 18 08:45:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e97_27958/03_2024/8e97_27958.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e97_27958/03_2024/8e97_27958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e97_27958/03_2024/8e97_27958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e97_27958/03_2024/8e97_27958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e97_27958/03_2024/8e97_27958.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e97_27958/03_2024/8e97_27958.pdb" } resolution = 4.19 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= 0.002 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 80 5.16 5 C 12872 2.51 5 N 3566 2.21 5 O 3856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 763": "NH1" <-> "NH2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "C ARG 673": "NH1" <-> "NH2" Residue "C ARG 704": "NH1" <-> "NH2" Residue "C ARG 763": "NH1" <-> "NH2" Residue "D GLU 549": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20374 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 5587 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 34, 'TRANS': 765} Chain breaks: 1 Unresolved non-hydrogen bonds: 753 Unresolved non-hydrogen angles: 915 Unresolved non-hydrogen dihedrals: 638 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 8, 'GLU:plan': 40, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 509 Chain: "B" Number of atoms: 5324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5324 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 39, 'TRANS': 693} Chain breaks: 3 Unresolved non-hydrogen bonds: 412 Unresolved non-hydrogen angles: 524 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 278 Chain: "C" Number of atoms: 4692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 4692 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 370} Link IDs: {'PTRANS': 33, 'TRANS': 723} Chain breaks: 1 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1371 Unresolved non-hydrogen angles: 1751 Unresolved non-hydrogen dihedrals: 1147 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 20, 'TYR:plan': 15, 'ASN:plan1': 26, 'TRP:plan': 6, 'HIS:plan': 13, 'PHE:plan': 13, 'GLU:plan': 34, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 785 Chain: "D" Number of atoms: 4564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 4564 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 422} Link IDs: {'PTRANS': 42, 'TRANS': 741} Chain breaks: 2 Unresolved chain link angles: 28 Unresolved non-hydrogen bonds: 1654 Unresolved non-hydrogen angles: 2124 Unresolved non-hydrogen dihedrals: 1424 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 17, 'TYR:plan': 17, 'ASN:plan1': 9, 'TRP:plan': 11, 'ASP:plan': 20, 'PHE:plan': 25, 'GLU:plan': 30, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 950 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.32, per 1000 atoms: 0.56 Number of scatterers: 20374 At special positions: 0 Unit cell: (172.056, 154.936, 185.752, 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 80 16.00 O 3856 8.00 N 3566 7.00 C 12872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.04 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.78 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 317 " distance=2.04 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.04 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.04 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.03 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 901 " - " ASN A 203 " " NAG A 902 " - " ASN A 350 " " NAG A 903 " - " ASN A 239 " " NAG A 904 " - " ASN A 276 " " NAG A 905 " - " ASN A 771 " " NAG A 906 " - " ASN A 368 " " NAG B 901 " - " ASN B 685 " " NAG C 901 " - " ASN C 471 " " NAG E 1 " - " ASN A 61 " " NAG F 1 " - " ASN B 337 " " NAG G 1 " - " ASN C 771 " Time building additional restraints: 8.47 Conformation dependent library (CDL) restraints added in 4.0 seconds 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5716 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 36 sheets defined 41.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 36 through 54 removed outlier: 3.776A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.915A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.933A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 4.625A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.766A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 278 through 297 removed outlier: 3.686A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 502 through 507 removed outlier: 4.139A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.554A pdb=" N GLN A 525 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 570 removed outlier: 3.974A pdb=" N VAL A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.827A pdb=" N MET A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 614 removed outlier: 3.502A pdb=" N MET A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 657 removed outlier: 3.564A pdb=" N GLY A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 645 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.533A pdb=" N ASN A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.984A pdb=" N ARG A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 707 removed outlier: 3.523A pdb=" N MET A 706 " --> pdb=" O MET A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 removed outlier: 3.722A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.561A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 783 removed outlier: 4.068A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 removed outlier: 3.619A pdb=" N ASP A 789 " --> pdb=" O MET A 785 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS A 790 " --> pdb=" O GLU A 786 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 834 removed outlier: 3.914A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE A 828 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 841 removed outlier: 3.904A pdb=" N HIS A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.820A pdb=" N ILE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 4.071A pdb=" N ILE B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 removed outlier: 4.106A pdb=" N VAL B 128 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 160 removed outlier: 4.524A pdb=" N VAL B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU B 158 " --> pdb=" O PHE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.548A pdb=" N PHE B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 229 through 242 removed outlier: 4.256A pdb=" N VAL B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.531A pdb=" N ARG B 282 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 307 removed outlier: 3.569A pdb=" N ARG B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 4.152A pdb=" N ARG B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 470 removed outlier: 3.778A pdb=" N LEU B 462 " --> pdb=" O CYS B 458 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL B 468 " --> pdb=" O LYS B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 599 through 611 Processing helix chain 'B' and resid 626 through 652 removed outlier: 3.532A pdb=" N LEU B 630 " --> pdb=" O LYS B 626 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 631 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 687 through 696 removed outlier: 4.069A pdb=" N SER B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN B 695 " --> pdb=" O ASN B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 709 through 720 Processing helix chain 'B' and resid 730 through 737 removed outlier: 4.020A pdb=" N TYR B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 782 removed outlier: 3.528A pdb=" N LEU B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 778 " --> pdb=" O ASP B 774 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE B 780 " --> pdb=" O ALA B 776 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 782 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 794 removed outlier: 3.707A pdb=" N LYS B 788 " --> pdb=" O GLY B 784 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 792 " --> pdb=" O LYS B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 801 removed outlier: 3.920A pdb=" N ASN B 800 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 801 " --> pdb=" O CYS B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 797 through 801' Processing helix chain 'B' and resid 814 through 831 removed outlier: 4.184A pdb=" N MET B 821 " --> pdb=" O GLY B 817 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 823 " --> pdb=" O PHE B 819 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 829 " --> pdb=" O ALA B 825 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 830 " --> pdb=" O MET B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 836 removed outlier: 3.842A pdb=" N TRP B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 54 removed outlier: 3.776A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.914A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.932A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 4.625A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.766A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 278 through 297 removed outlier: 3.687A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 326 Processing helix chain 'C' and resid 457 through 471 removed outlier: 3.705A pdb=" N ILE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.756A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.481A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 554 removed outlier: 3.656A pdb=" N SER C 553 " --> pdb=" O SER C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 582 removed outlier: 3.632A pdb=" N GLY C 567 " --> pdb=" O TRP C 563 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 579 " --> pdb=" O VAL C 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 580 " --> pdb=" O MET C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 614 removed outlier: 3.800A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP C 611 " --> pdb=" O MET C 607 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY C 612 " --> pdb=" O TRP C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.637A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 652 " --> pdb=" O THR C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.510A pdb=" N PHE C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.712A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET C 706 " --> pdb=" O MET C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 710 No H-bonds generated for 'chain 'C' and resid 708 through 710' Processing helix chain 'C' and resid 713 through 722 removed outlier: 3.631A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 721 " --> pdb=" O ALA C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 743 removed outlier: 3.576A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 740 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 743 " --> pdb=" O GLU C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.810A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS C 780 " --> pdb=" O ILE C 776 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.583A pdb=" N ASP C 789 " --> pdb=" O MET C 785 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP C 792 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 73 through 88 removed outlier: 3.819A pdb=" N ILE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 4.070A pdb=" N ILE D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU D 108 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN D 114 " --> pdb=" O PHE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 removed outlier: 4.105A pdb=" N VAL D 128 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.523A pdb=" N VAL D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU D 158 " --> pdb=" O PHE D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 186 removed outlier: 3.550A pdb=" N PHE D 178 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 182 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 218 Processing helix chain 'D' and resid 229 through 242 removed outlier: 4.257A pdb=" N VAL D 235 " --> pdb=" O GLU D 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 removed outlier: 4.531A pdb=" N ARG D 282 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 307 removed outlier: 3.570A pdb=" N ARG D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 335 removed outlier: 4.152A pdb=" N ARG D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 3.511A pdb=" N ASP D 460 " --> pdb=" O GLY D 456 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.671A pdb=" N GLU D 497 " --> pdb=" O GLY D 493 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 4.028A pdb=" N GLU D 518 " --> pdb=" O GLU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 576 removed outlier: 3.767A pdb=" N MET D 558 " --> pdb=" O ALA D 554 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 611 removed outlier: 4.231A pdb=" N VAL D 603 " --> pdb=" O ILE D 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 605 " --> pdb=" O LYS D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 651 removed outlier: 3.681A pdb=" N VAL D 629 " --> pdb=" O SER D 625 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL D 631 " --> pdb=" O ILE D 627 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 639 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR D 644 " --> pdb=" O LEU D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 692 removed outlier: 3.785A pdb=" N ASN D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 687 through 692' Processing helix chain 'D' and resid 696 through 701 removed outlier: 4.419A pdb=" N HIS D 700 " --> pdb=" O TYR D 696 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR D 701 " --> pdb=" O ARG D 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 696 through 701' Processing helix chain 'D' and resid 711 through 721 removed outlier: 4.213A pdb=" N SER D 717 " --> pdb=" O ASP D 713 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS D 719 " --> pdb=" O LEU D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 739 removed outlier: 3.546A pdb=" N ASN D 734 " --> pdb=" O ALA D 730 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 783 Processing helix chain 'D' and resid 784 through 791 removed outlier: 4.554A pdb=" N LYS D 788 " --> pdb=" O GLY D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 834 removed outlier: 4.283A pdb=" N MET D 821 " --> pdb=" O GLY D 817 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 825 " --> pdb=" O MET D 821 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N MET D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 831 " --> pdb=" O GLY D 827 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA D 834 " --> pdb=" O LEU D 830 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 5.958A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 196 removed outlier: 5.467A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 165 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 195 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 219 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 248 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.675A pdb=" N ILE A 353 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 478 removed outlier: 7.188A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.752A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.594A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.708A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.895A pdb=" N PHE B 36 " --> pdb=" O VAL B 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 194 through 200 removed outlier: 8.193A pdb=" N PHE B 165 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 198 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 167 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N THR B 200 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR B 169 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 164 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL B 225 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA B 166 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 227 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 168 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 274 through 277 removed outlier: 3.561A pdb=" N ALA B 362 " --> pdb=" O GLU B 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AB5, first strand: chain 'B' and resid 375 through 376 removed outlier: 3.947A pdb=" N GLU B 376 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 379 " --> pdb=" O GLU B 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 403 through 407 removed outlier: 3.904A pdb=" N ASP B 474 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 407 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ARG B 434 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 414 through 417 Processing sheet with id=AB8, first strand: chain 'B' and resid 486 through 487 Processing sheet with id=AB9, first strand: chain 'B' and resid 680 through 681 removed outlier: 6.349A pdb=" N GLY B 681 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ASP B 729 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 746 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 680 through 681 removed outlier: 6.349A pdb=" N GLY B 681 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ASP B 729 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE B 531 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ALA B 755 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 31 through 33 Processing sheet with id=AC3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.957A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 192 through 196 removed outlier: 5.466A pdb=" N LYS C 193 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 165 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 195 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 219 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 248 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 269 through 271 removed outlier: 3.674A pdb=" N ILE C 353 " --> pdb=" O GLY C 365 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS C 371 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 400 through 401 Processing sheet with id=AC7, first strand: chain 'C' and resid 410 through 412 removed outlier: 3.560A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC9, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.434A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.434A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.896A pdb=" N PHE D 36 " --> pdb=" O VAL D 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 194 through 200 removed outlier: 8.195A pdb=" N PHE D 165 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL D 198 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL D 167 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N THR D 200 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR D 169 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA D 164 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL D 225 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA D 166 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR D 227 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE D 168 " --> pdb=" O TYR D 227 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 274 through 277 removed outlier: 3.562A pdb=" N ALA D 362 " --> pdb=" O GLU D 370 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AD6, first strand: chain 'D' and resid 375 through 376 removed outlier: 3.946A pdb=" N GLU D 376 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 379 " --> pdb=" O GLU D 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 476 through 477 removed outlier: 5.504A pdb=" N VAL D 405 " --> pdb=" O TYR D 476 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 415 through 417 removed outlier: 3.799A pdb=" N LEU D 452 " --> pdb=" O CYS D 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 531 through 535 759 hydrogen bonds defined for protein. 2151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.57 Time building geometry restraints manager: 9.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3447 1.30 - 1.44: 5303 1.44 - 1.57: 11859 1.57 - 1.70: 1 1.70 - 1.84: 126 Bond restraints: 20736 Sorted by residual: bond pdb=" C PRO B 388 " pdb=" O PRO B 388 " ideal model delta sigma weight residual 1.233 1.167 0.065 1.16e-02 7.43e+03 3.18e+01 bond pdb=" N ASP D 399 " pdb=" CA ASP D 399 " ideal model delta sigma weight residual 1.458 1.494 -0.035 6.30e-03 2.52e+04 3.11e+01 bond pdb=" C PRO B 396 " pdb=" O PRO B 396 " ideal model delta sigma weight residual 1.235 1.167 0.068 1.30e-02 5.92e+03 2.73e+01 bond pdb=" C ALA B 608 " pdb=" O ALA B 608 " ideal model delta sigma weight residual 1.237 1.294 -0.057 1.17e-02 7.31e+03 2.41e+01 bond pdb=" N TRP C 636 " pdb=" CA TRP C 636 " ideal model delta sigma weight residual 1.459 1.406 0.053 1.21e-02 6.83e+03 1.90e+01 ... (remaining 20731 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.59: 439 105.59 - 112.76: 11535 112.76 - 119.93: 6570 119.93 - 127.10: 9707 127.10 - 134.27: 246 Bond angle restraints: 28497 Sorted by residual: angle pdb=" C GLN B 395 " pdb=" CA GLN B 395 " pdb=" CB GLN B 395 " ideal model delta sigma weight residual 110.17 130.24 -20.07 1.97e+00 2.58e-01 1.04e+02 angle pdb=" N VAL B 610 " pdb=" CA VAL B 610 " pdb=" C VAL B 610 " ideal model delta sigma weight residual 110.42 118.82 -8.40 9.60e-01 1.09e+00 7.66e+01 angle pdb=" N TRP D 607 " pdb=" CA TRP D 607 " pdb=" C TRP D 607 " ideal model delta sigma weight residual 111.07 101.89 9.18 1.07e+00 8.73e-01 7.36e+01 angle pdb=" CA TRP C 636 " pdb=" CB TRP C 636 " pdb=" CG TRP C 636 " ideal model delta sigma weight residual 113.60 100.29 13.31 1.90e+00 2.77e-01 4.91e+01 angle pdb=" O VAL A 793 " pdb=" C VAL A 793 " pdb=" N ARG A 794 " ideal model delta sigma weight residual 122.11 131.18 -9.07 1.30e+00 5.92e-01 4.86e+01 ... (remaining 28492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.06: 11720 24.06 - 48.13: 525 48.13 - 72.19: 52 72.19 - 96.26: 13 96.26 - 120.32: 7 Dihedral angle restraints: 12317 sinusoidal: 3479 harmonic: 8838 Sorted by residual: dihedral pdb=" C GLN B 395 " pdb=" N GLN B 395 " pdb=" CA GLN B 395 " pdb=" CB GLN B 395 " ideal model delta harmonic sigma weight residual -122.60 -159.37 36.77 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" N GLN B 395 " pdb=" C GLN B 395 " pdb=" CA GLN B 395 " pdb=" CB GLN B 395 " ideal model delta harmonic sigma weight residual 122.80 155.00 -32.20 0 2.50e+00 1.60e-01 1.66e+02 dihedral pdb=" CA VAL D 90 " pdb=" C VAL D 90 " pdb=" N HIS D 91 " pdb=" CA HIS D 91 " ideal model delta harmonic sigma weight residual 180.00 131.41 48.59 0 5.00e+00 4.00e-02 9.45e+01 ... (remaining 12314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 3550 0.304 - 0.607: 11 0.607 - 0.911: 1 0.911 - 1.215: 0 1.215 - 1.518: 2 Chirality restraints: 3564 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.88 -1.52 2.00e-02 2.50e+03 5.76e+03 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.13e+02 chirality pdb=" CA GLN B 395 " pdb=" N GLN B 395 " pdb=" C GLN B 395 " pdb=" CB GLN B 395 " both_signs ideal model delta sigma weight residual False 2.51 1.04 1.47 2.00e-01 2.50e+01 5.42e+01 ... (remaining 3561 not shown) Planarity restraints: 3722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 906 " -0.295 2.00e-02 2.50e+03 2.48e-01 7.69e+02 pdb=" C7 NAG A 906 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG A 906 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A 906 " 0.423 2.00e-02 2.50e+03 pdb=" O7 NAG A 906 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.141 2.00e-02 2.50e+03 1.16e-01 1.69e+02 pdb=" C7 NAG F 2 " 0.039 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.105 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.186 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 905 " -0.068 2.00e-02 2.50e+03 5.55e-02 3.85e+01 pdb=" C7 NAG A 905 " 0.020 2.00e-02 2.50e+03 pdb=" C8 NAG A 905 " -0.052 2.00e-02 2.50e+03 pdb=" N2 NAG A 905 " 0.087 2.00e-02 2.50e+03 pdb=" O7 NAG A 905 " 0.013 2.00e-02 2.50e+03 ... (remaining 3719 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 83 2.44 - 3.05: 14560 3.05 - 3.67: 27774 3.67 - 4.28: 37432 4.28 - 4.90: 59714 Nonbonded interactions: 139563 Sorted by model distance: nonbonded pdb=" O MET C 394 " pdb=" O SER C 395 " model vdw 1.822 3.040 nonbonded pdb=" OG SER A 713 " pdb=" CB GLU A 716 " model vdw 1.867 3.440 nonbonded pdb=" CB VAL B 610 " pdb=" CZ3 TRP B 632 " model vdw 1.927 3.770 nonbonded pdb=" C VAL B 610 " pdb=" CZ3 TRP B 632 " model vdw 1.942 3.570 nonbonded pdb=" C VAL B 610 " pdb=" CH2 TRP B 632 " model vdw 2.027 3.570 ... (remaining 139558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 25 through 29 and (name N or name CA or name C or name O \ or name CB )) or (resid 30 through 53 and (name N or name CA or name C or name O \ or name CB )) or resid 54 or (resid 55 through 111 and (name N or name CA or na \ me C or name O or name CB )) or resid 112 or (resid 113 through 119 and (name N \ or name CA or name C or name O or name CB )) or resid 120 or (resid 121 through \ 172 and (name N or name CA or name C or name O or name CB )) or resid 173 or (re \ sid 174 through 199 and (name N or name CA or name C or name O or name CB )) or \ resid 200 or (resid 201 through 241 and (name N or name CA or name C or name O o \ r name CB )) or resid 242 or (resid 243 and (name N or name CA or name C or name \ O or name CB )) or resid 244 or (resid 245 through 249 and (name N or name CA o \ r name C or name O or name CB )) or (resid 250 through 255 and (name N or name C \ A or name C or name O or name CB )) or (resid 256 through 264 and (name N or nam \ e CA or name C or name O or name CB )) or resid 265 or (resid 266 through 267 an \ d (name N or name CA or name C or name O or name CB )) or resid 268 or (resid 26 \ 9 through 273 and (name N or name CA or name C or name O or name CB )) or resid \ 274 or (resid 275 through 285 and (name N or name CA or name C or name O or name \ CB )) or resid 286 or (resid 287 through 306 and (name N or name CA or name C o \ r name O or name CB )) or resid 307 or (resid 308 through 309 and (name N or nam \ e CA or name C or name O or name CB )) or resid 310 or (resid 311 through 317 an \ d (name N or name CA or name C or name O or name CB )) or resid 318 or (resid 31 \ 9 through 332 and (name N or name CA or name C or name O or name CB )) or resid \ 333 or (resid 334 through 335 and (name N or name CA or name C or name O or name \ CB )) or (resid 336 through 343 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 344 through 364 and (name N or name CA or name C or name O o \ r name CB )) or resid 365 or (resid 366 through 368 and (name N or name CA or na \ me C or name O or name CB )) or resid 369 or (resid 370 through 382 and (name N \ or name CA or name C or name O or name CB )) or (resid 383 through 390 and (name \ N or name CA or name C or name O or name CB )) or resid 391 or (resid 392 throu \ gh 396 and (name N or name CA or name C or name O or name CB )) or resid 397 thr \ ough 445 or (resid 446 and (name N or name CA or name C or name O or name CB )) \ or resid 447 through 482 or (resid 483 and (name N or name CA or name C or name \ O or name CB )) or resid 484 through 578 or (resid 579 and (name N or name CA or \ name C or name O or name CB )) or resid 580 through 662 or (resid 663 and (name \ N or name CA or name C or name O or name CB )) or resid 664 through 667 or (res \ id 668 and (name N or name CA or name C or name O or name CB )) or resid 669 thr \ ough 798 or resid 906)) selection = (chain 'C' and (resid 25 through 398 or (resid 399 and (name N or name CA or nam \ e C or name O or name CB )) or resid 400 through 411 or (resid 412 and (name N o \ r name CA or name C or name O or name CB )) or resid 413 through 421 or (resid 4 \ 22 through 423 and (name N or name CA or name C or name O or name CB )) or resid \ 424 or (resid 425 through 427 and (name N or name CA or name C or name O or nam \ e CB )) or resid 428 or (resid 429 and (name N or name CA or name C or name O or \ name CB )) or resid 430 through 431 or (resid 432 through 433 and (name N or na \ me CA or name C or name O or name CB )) or resid 434 through 467 or (resid 468 a \ nd (name N or name CA or name C or name O or name CB )) or resid 469 through 474 \ or (resid 475 and (name N or name CA or name C or name O or name CB )) or resid \ 476 through 489 or (resid 490 through 497 and (name N or name CA or name C or n \ ame O or name CB )) or resid 498 through 521 or (resid 522 and (name N or name C \ A or name C or name O or name CB )) or resid 523 through 542 or (resid 543 throu \ gh 545 and (name N or name CA or name C or name O or name CB )) or resid 546 thr \ ough 547 or (resid 548 and (name N or name CA or name C or name O or name CB )) \ or resid 549 through 550 or (resid 551 through 552 and (name N or name CA or nam \ e C or name O or name CB )) or resid 553 through 562 or (resid 563 and (name N o \ r name CA or name C or name O or name CB )) or resid 564 through 633 or (resid 6 \ 34 and (name N or name CA or name C or name O or name CB )) or resid 635 through \ 673 or (resid 674 and (name N or name CA or name C or name O or name CB )) or r \ esid 675 through 677 or (resid 678 and (name N or name CA or name C or name O or \ name CB )) or resid 679 through 693 or (resid 694 through 696 and (name N or na \ me CA or name C or name O or name CB )) or resid 697 through 703 or (resid 704 a \ nd (name N or name CA or name C or name O or name CB )) or resid 705 through 706 \ or (resid 707 through 708 and (name N or name CA or name C or name O or name CB \ )) or resid 709 through 718 or (resid 719 through 720 and (name N or name CA or \ name C or name O or name CB )) or resid 721 through 724 or (resid 725 and (name \ N or name CA or name C or name O or name CB )) or resid 726 through 736 or (res \ id 737 and (name N or name CA or name C or name O or name CB )) or resid 738 thr \ ough 763 or (resid 764 and (name N or name CA or name C or name O or name CB )) \ or resid 765 through 768 or (resid 769 and (name N or name CA or name C or name \ O or name CB )) or resid 770 through 780 or (resid 781 and (name N or name CA or \ name C or name O or name CB )) or resid 782 through 784 or (resid 785 through 7 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 788 or (res \ id 789 and (name N or name CA or name C or name O or name CB )) or resid 790 thr \ ough 798 or resid 901)) } ncs_group { reference = (chain 'B' and ((resid 31 through 39 and (name N or name CA or name C or name O \ or name CB )) or resid 40 or (resid 41 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 or (resid 69 through 82 and (name N or na \ me CA or name C or name O or name CB )) or resid 83 or (resid 84 through 85 and \ (name N or name CA or name C or name O or name CB )) or (resid 86 through 91 and \ (name N or name CA or name C or name O or name CB )) or resid 92 or (resid 93 t \ hrough 123 and (name N or name CA or name C or name O or name CB )) or resid 124 \ through 125 or (resid 126 through 135 and (name N or name CA or name C or name \ O or name CB )) or resid 136 or (resid 137 through 142 and (name N or name CA or \ name C or name O or name CB )) or resid 143 or (resid 144 through 173 and (name \ N or name CA or name C or name O or name CB )) or resid 174 or (resid 175 throu \ gh 180 and (name N or name CA or name C or name O or name CB )) or resid 181 or \ (resid 182 through 203 and (name N or name CA or name C or name O or name CB )) \ or resid 204 or (resid 205 and (name N or name CA or name C or name O or name CB \ )) or resid 206 through 207 or (resid 208 through 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 or (resid 245 through 246 and (name \ N or name CA or name C or name O or name CB )) or resid 247 or (resid 248 and ( \ name N or name CA or name C or name O or name CB )) or resid 249 or (resid 250 t \ hrough 259 and (name N or name CA or name C or name O or name CB )) or resid 260 \ or (resid 261 through 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 or (resid 273 through 291 and (name N or name CA or name C or n \ ame O or name CB )) or resid 292 or (resid 293 through 298 and (name N or name C \ A or name C or name O or name CB )) or (resid 299 through 307 and (name N or nam \ e CA or name C or name O or name CB )) or resid 308 or (resid 309 through 314 an \ d (name N or name CA or name C or name O or name CB )) or (resid 315 through 321 \ and (name N or name CA or name C or name O or name CB )) or resid 322 or (resid \ 323 through 341 and (name N or name CA or name C or name O or name CB )) or res \ id 342 or (resid 343 through 349 and (name N or name CA or name C or name O or n \ ame CB )) or resid 350 through 351 or (resid 352 through 372 and (name N or name \ CA or name C or name O or name CB )) or resid 373 or (resid 374 through 377 and \ (name N or name CA or name C or name O or name CB )) or resid 378 or (resid 379 \ through 402 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 03 through 410 or (resid 411 and (name N or name CA or name C or name O or name \ CB )) or resid 412 through 433 or (resid 434 through 435 and (name N or name CA \ or name C or name O or name CB )) or resid 436 through 448 or (resid 449 and (na \ me N or name CA or name C or name O or name CB )) or resid 450 or (resid 451 and \ (name N or name CA or name C or name O or name CB )) or resid 452 through 454 o \ r (resid 455 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 56 through 462 or (resid 463 through 464 and (name N or name CA or name C or nam \ e O or name CB )) or resid 465 through 466 or (resid 467 and (name N or name CA \ or name C or name O or name CB )) or resid 468 through 469 or (resid 470 through \ 471 and (name N or name CA or name C or name O or name CB )) or resid 472 throu \ gh 481 or (resid 482 and (name N or name CA or name C or name O or name CB )) or \ resid 483 through 484 or (resid 485 through 486 and (name N or name CA or name \ C or name O or name CB )) or resid 487 or (resid 488 and (name N or name CA or n \ ame C or name O or name CB )) or resid 489 through 493 or (resid 494 and (name N \ or name CA or name C or name O or name CB )) or resid 495 through 498 or (resid \ 499 through 503 and (name N or name CA or name C or name O or name CB )) or res \ id 504 or (resid 505 through 506 and (name N or name CA or name C or name O or n \ ame CB )) or resid 507 through 513 or (resid 514 through 516 and (name N or name \ CA or name C or name O or name CB )) or resid 517 or (resid 518 and (name N or \ name CA or name C or name O or name CB )) or resid 519 through 527 or (resid 528 \ and (name N or name CA or name C or name O or name CB )) or resid 529 through 6 \ 33 or (resid 634 and (name N or name CA or name C or name O or name CB )) or res \ id 635 through 652 or (resid 653 through 656 and (name N or name CA or name C or \ name O or name CB )) or resid 657 through 664 or (resid 665 through 667 and (na \ me N or name CA or name C or name O or name CB )) or resid 668 through 671 or (r \ esid 672 through 675 and (name N or name CA or name C or name O or name CB )) or \ resid 676 through 677 or (resid 678 through 679 and (name N or name CA or name \ C or name O or name CB )) or resid 680 through 689 or (resid 690 and (name N or \ name CA or name C or name O or name CB )) or resid 691 through 692 or (resid 693 \ and (name N or name CA or name C or name O or name CB )) or resid 694 or (resid \ 695 and (name N or name CA or name C or name O or name CB )) or resid 696 throu \ gh 697 or (resid 698 and (name N or name CA or name C or name O or name CB )) or \ resid 699 through 704 or (resid 705 through 706 and (name N or name CA or name \ C or name O or name CB )) or resid 707 through 711 or (resid 712 through 714 and \ (name N or name CA or name C or name O or name CB )) or resid 715 through 717 o \ r (resid 718 through 720 and (name N or name CA or name C or name O or name CB ) \ ) or resid 721 through 728 or (resid 729 through 731 and (name N or name CA or n \ ame C or name O or name CB )) or resid 732 through 734 or (resid 735 and (name N \ or name CA or name C or name O or name CB )) or resid 736 through 738 or (resid \ 739 and (name N or name CA or name C or name O or name CB )) or resid 740 throu \ gh 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) or \ resid 749 through 751 or (resid 752 and (name N or name CA or name C or name O \ or name CB )) or resid 753 through 762 or (resid 763 through 766 and (name N or \ name CA or name C or name O or name CB )) or resid 767 or (resid 768 and (name N \ or name CA or name C or name O or name CB )) or resid 769 or (resid 770 through \ 772 and (name N or name CA or name C or name O or name CB )) or resid 773 throu \ gh 774 or (resid 775 through 776 and (name N or name CA or name C or name O or n \ ame CB )) or resid 777 through 778 or (resid 779 and (name N or name CA or name \ C or name O or name CB )) or resid 780 through 784 or (resid 785 and (name N or \ name CA or name C or name O or name CB )) or resid 786 through 787 or (resid 788 \ and (name N or name CA or name C or name O or name CB )) or resid 789 through 7 \ 98 or (resid 799 through 804 and (name N or name CA or name C or name O or name \ CB )) or resid 805 through 819 or (resid 820 through 821 and (name N or name CA \ or name C or name O or name CB )) or resid 822 through 827 or (resid 828 through \ 841 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 31 through 408 or (resid 409 through 411 and (name N or na \ me CA or name C or name O or name CB )) or resid 412 through 416 or (resid 417 a \ nd (name N or name CA or name C or name O or name CB )) or resid 418 through 437 \ or resid 447 through 537 or resid 598 through 602 or (resid 603 through 611 and \ (name N or name CA or name C or name O or name CB )) or resid 612 through 613 o \ r resid 623 through 666 or (resid 667 and (name N or name CA or name C or name O \ or name CB )) or resid 668 through 672 or (resid 673 through 675 and (name N or \ name CA or name C or name O or name CB )) or resid 676 through 809 or (resid 81 \ 0 through 812 and (name N or name CA or name C or name O or name CB )) or resid \ 813 through 818 or (resid 819 through 821 and (name N or name CA or name C or na \ me O or name CB )) or resid 822 through 829 or (resid 830 through 841 and (name \ N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.080 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 56.830 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.120 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 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 : 0.007 0.113 20736 Z= 0.491 Angle : 1.057 20.074 28497 Z= 0.660 Chirality : 0.069 1.518 3564 Planarity : 0.007 0.248 3711 Dihedral : 14.168 120.324 6562 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.69 % Allowed : 13.37 % Favored : 85.94 % Rotamer: Outliers : 1.35 % Allowed : 9.29 % Favored : 89.36 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.51 % 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: -5.58 (0.11), residues: 3052 helix: -3.58 (0.11), residues: 1066 sheet: -3.27 (0.24), residues: 328 loop : -4.02 (0.12), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 247 HIS 0.012 0.002 HIS B 334 PHE 0.023 0.002 PHE D 413 TYR 0.058 0.002 TYR B 390 ARG 0.006 0.001 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 239 time to evaluate : 2.262 Fit side-chains revert: symmetry clash REVERT: A 646 SER cc_start: 0.9402 (m) cc_final: 0.9022 (t) REVERT: B 699 MET cc_start: 0.6367 (mtp) cc_final: 0.6136 (ttm) REVERT: C 461 ASP cc_start: 0.9029 (t0) cc_final: 0.8717 (t0) REVERT: C 470 MET cc_start: 0.9050 (mmm) cc_final: 0.8329 (mmm) REVERT: C 528 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8042 (tm-30) REVERT: C 636 TRP cc_start: 0.8892 (OUTLIER) cc_final: 0.8082 (t60) REVERT: C 785 MET cc_start: 0.8928 (mmm) cc_final: 0.8449 (mmm) outliers start: 21 outliers final: 9 residues processed: 259 average time/residue: 0.2644 time to fit residues: 111.8797 Evaluate side-chains 158 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 20.0000 chunk 231 optimal weight: 50.0000 chunk 128 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 239 optimal weight: 50.0000 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 277 optimal weight: 0.0670 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 47 ASN A 134 HIS A 146 HIS A 147 GLN A 177 GLN A 363 GLN A 405 GLN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN B 151 GLN B 213 GLN B 334 HIS B 700 HIS C 477 HIS C 674 ASN ** C 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 GLN ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 HIS ** D 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20736 Z= 0.285 Angle : 0.748 9.298 28497 Z= 0.394 Chirality : 0.048 0.301 3564 Planarity : 0.005 0.064 3711 Dihedral : 8.305 69.937 3493 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.40 % Favored : 88.37 % Rotamer: Outliers : 0.32 % Allowed : 7.76 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.03 % Twisted General : 0.17 % 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: -4.00 (0.13), residues: 3052 helix: -1.77 (0.14), residues: 1097 sheet: -2.94 (0.23), residues: 390 loop : -3.30 (0.14), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 247 HIS 0.006 0.002 HIS A 780 PHE 0.022 0.002 PHE C 472 TYR 0.026 0.002 TYR A 681 ARG 0.009 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 SER cc_start: 0.9319 (m) cc_final: 0.8932 (t) REVERT: C 461 ASP cc_start: 0.8835 (t0) cc_final: 0.8560 (t0) REVERT: C 470 MET cc_start: 0.8871 (mmm) cc_final: 0.8533 (mmm) REVERT: C 639 PHE cc_start: 0.8445 (t80) cc_final: 0.8178 (t80) REVERT: D 699 MET cc_start: 0.4533 (mpp) cc_final: 0.4050 (mpp) REVERT: D 746 VAL cc_start: 0.7333 (p) cc_final: 0.7115 (p) REVERT: D 824 VAL cc_start: 0.5250 (m) cc_final: 0.5024 (p) outliers start: 5 outliers final: 3 residues processed: 189 average time/residue: 0.2425 time to fit residues: 79.1792 Evaluate side-chains 145 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 231 optimal weight: 50.0000 chunk 189 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 247 optimal weight: 50.0000 chunk 276 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 487 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN B 672 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 HIS D 700 HIS ** D 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20736 Z= 0.360 Angle : 0.756 9.990 28497 Z= 0.394 Chirality : 0.049 0.242 3564 Planarity : 0.005 0.057 3711 Dihedral : 7.587 59.039 3493 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.98 % Favored : 88.79 % Rotamer: Outliers : 0.38 % Allowed : 8.40 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.10 % 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: -3.31 (0.14), residues: 3052 helix: -1.17 (0.15), residues: 1135 sheet: -2.38 (0.24), residues: 379 loop : -3.01 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 381 HIS 0.008 0.002 HIS D 700 PHE 0.023 0.002 PHE A 810 TYR 0.029 0.002 TYR A 681 ARG 0.005 0.001 ARG C 722 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 SER cc_start: 0.9396 (m) cc_final: 0.8946 (t) REVERT: C 461 ASP cc_start: 0.8796 (t0) cc_final: 0.8583 (t0) REVERT: C 470 MET cc_start: 0.8891 (mmm) cc_final: 0.8448 (mmm) REVERT: C 568 LEU cc_start: 0.8022 (pp) cc_final: 0.7808 (tt) REVERT: D 639 PHE cc_start: 0.7421 (p90) cc_final: 0.7095 (p90) REVERT: D 699 MET cc_start: 0.4734 (mpp) cc_final: 0.4108 (mpp) REVERT: D 746 VAL cc_start: 0.7456 (p) cc_final: 0.7166 (p) outliers start: 6 outliers final: 3 residues processed: 173 average time/residue: 0.2384 time to fit residues: 71.8696 Evaluate side-chains 140 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 20.0000 chunk 209 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 279 optimal weight: 0.3980 chunk 295 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 264 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN B 287 GLN B 334 HIS ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20736 Z= 0.169 Angle : 0.632 10.958 28497 Z= 0.327 Chirality : 0.045 0.242 3564 Planarity : 0.004 0.056 3711 Dihedral : 6.730 57.687 3493 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.98 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.67 (0.15), residues: 3052 helix: -0.52 (0.15), residues: 1136 sheet: -2.15 (0.24), residues: 403 loop : -2.70 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 381 HIS 0.005 0.001 HIS B 116 PHE 0.019 0.001 PHE A 810 TYR 0.012 0.001 TYR A 703 ARG 0.002 0.000 ARG C 468 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8658 (tp30) cc_final: 0.7974 (tm-30) REVERT: A 157 VAL cc_start: 0.8268 (t) cc_final: 0.7990 (p) REVERT: A 646 SER cc_start: 0.9348 (m) cc_final: 0.8936 (t) REVERT: B 403 LEU cc_start: 0.8395 (pp) cc_final: 0.8095 (pt) REVERT: B 462 LEU cc_start: 0.9478 (pp) cc_final: 0.9192 (tt) REVERT: B 471 PHE cc_start: 0.7872 (m-10) cc_final: 0.7571 (m-10) REVERT: B 763 MET cc_start: 0.7936 (mtp) cc_final: 0.7711 (mtm) REVERT: C 470 MET cc_start: 0.8615 (mmm) cc_final: 0.8054 (mmm) REVERT: D 639 PHE cc_start: 0.7331 (p90) cc_final: 0.7068 (p90) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2451 time to fit residues: 84.2230 Evaluate side-chains 147 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5659 > 50: distance: 14 - 33: 3.825 distance: 18 - 38: 6.575 distance: 22 - 46: 3.349 distance: 27 - 33: 3.641 distance: 34 - 35: 4.358 distance: 34 - 37: 3.110 distance: 35 - 36: 3.114 distance: 38 - 39: 4.950 distance: 39 - 40: 6.178 distance: 39 - 42: 3.887 distance: 40 - 41: 4.277 distance: 40 - 46: 6.183 distance: 46 - 47: 9.941 distance: 47 - 48: 9.888 distance: 48 - 49: 16.316 distance: 48 - 50: 5.341 distance: 49 - 71: 11.980 distance: 50 - 51: 5.020 distance: 51 - 52: 6.911 distance: 51 - 54: 5.776 distance: 52 - 53: 15.112 distance: 52 - 61: 13.942 distance: 53 - 76: 9.842 distance: 54 - 55: 8.660 distance: 55 - 56: 3.906 distance: 55 - 57: 5.128 distance: 56 - 58: 7.503 distance: 57 - 59: 6.798 distance: 58 - 60: 4.337 distance: 59 - 60: 4.974 distance: 61 - 62: 18.633 distance: 62 - 63: 26.420 distance: 62 - 65: 7.999 distance: 63 - 64: 20.772 distance: 63 - 66: 15.900 distance: 66 - 67: 6.008 distance: 67 - 68: 6.630 distance: 67 - 70: 3.688 distance: 68 - 69: 5.206 distance: 68 - 71: 5.158 distance: 71 - 72: 7.564 distance: 72 - 75: 6.385 distance: 73 - 74: 3.777 distance: 73 - 76: 5.007 distance: 76 - 77: 4.297 distance: 77 - 78: 5.399 distance: 77 - 80: 4.492 distance: 78 - 84: 5.452 distance: 81 - 82: 8.101 distance: 81 - 83: 10.584 distance: 84 - 85: 6.019 distance: 85 - 86: 8.791 distance: 85 - 88: 4.520 distance: 86 - 87: 8.285 distance: 86 - 89: 6.401 distance: 87 - 113: 5.099 distance: 89 - 90: 4.133 distance: 90 - 91: 3.914 distance: 91 - 98: 3.216 distance: 92 - 120: 5.133 distance: 93 - 94: 3.904 distance: 94 - 95: 4.466 distance: 96 - 97: 6.377