Starting phenix.real_space_refine on Sun Sep 29 11:37:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i92_35255/09_2024/8i92_35255.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i92_35255/09_2024/8i92_35255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i92_35255/09_2024/8i92_35255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i92_35255/09_2024/8i92_35255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i92_35255/09_2024/8i92_35255.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i92_35255/09_2024/8i92_35255.cif" } resolution = 3.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 128 5.16 5 C 14476 2.51 5 N 3568 2.21 5 O 4170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22344 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6096 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "B" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "C" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6096 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "D" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "E" 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: "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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.55, per 1000 atoms: 0.56 Number of scatterers: 22344 At special positions: 0 Unit cell: (109.787, 135.875, 183.703, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 128 16.00 O 4170 8.00 N 3568 7.00 C 14476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 383 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 383 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False amino acid link not found "ATOM 5959 SD MET A 750 .*. S " "ATOM 7681 SG CYS B 203 .*. S " amino acid link not found "ATOM 16854 SD MET C 750 .*. S " "ATOM 18576 SG CYS D 203 .*. S " Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 901 " - " ASN A 322 " " NAG B 702 " - " ASN B 182 " " NAG B 703 " - " ASN B 158 " " NAG B 704 " - " ASN B 368 " " NAG B 705 " - " ASN B 354 " " NAG C 901 " - " ASN C 322 " " NAG D 702 " - " ASN D 182 " " NAG D 703 " - " ASN D 158 " " NAG D 704 " - " ASN D 368 " " NAG D 705 " - " ASN D 354 " " NAG E 1 " - " ASN A 53 " " NAG F 1 " - " ASN A 90 " " NAG G 1 " - " ASN A 103 " " NAG H 1 " - " ASN A 432 " " NAG I 1 " - " ASN A 546 " " NAG J 1 " - " ASN A 690 " " NAG K 1 " - " ASN B 258 " " NAG L 1 " - " ASN C 53 " " NAG M 1 " - " ASN C 90 " " NAG N 1 " - " ASN C 103 " " NAG O 1 " - " ASN C 432 " " NAG P 1 " - " ASN C 546 " " NAG Q 1 " - " ASN C 690 " " NAG R 1 " - " ASN D 258 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.13 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 378 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 374 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 378 " 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5088 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 12 sheets defined 65.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.251A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 4.021A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 4.090A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.943A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.618A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.712A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 193 removed outlier: 4.248A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.760A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 removed outlier: 3.827A pdb=" N GLU A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 220 through 230 removed outlier: 4.064A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.534A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.969A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.697A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.088A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.915A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.855A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.478A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.602A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.641A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.578A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 513 through 534 removed outlier: 3.900A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.731A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.820A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.577A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.752A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.619A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.644A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 716 removed outlier: 3.617A pdb=" N VAL A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 767 removed outlier: 4.081A pdb=" N ILE A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 27 through 31 removed outlier: 4.076A pdb=" N SER B 30 " --> pdb=" O GLU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 49 removed outlier: 3.588A pdb=" N CYS B 49 " --> pdb=" O CYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 removed outlier: 4.065A pdb=" N TYR B 60 " --> pdb=" O TRP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 81 Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 142 removed outlier: 3.959A pdb=" N GLY B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 134 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.887A pdb=" N LEU B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 227 removed outlier: 3.691A pdb=" N ALA B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 removed outlier: 3.935A pdb=" N THR B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.204A pdb=" N THR B 256 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 279 removed outlier: 3.830A pdb=" N TRP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 299 through 349 Processing helix chain 'B' and resid 359 through 371 Processing helix chain 'B' and resid 371 through 377 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 446 removed outlier: 3.504A pdb=" N TRP B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL B 439 " --> pdb=" O ASN B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 454 through 470 removed outlier: 3.939A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.543A pdb=" N LEU B 475 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 490 removed outlier: 3.659A pdb=" N TRP B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 490 " --> pdb=" O ASP B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 508 removed outlier: 4.489A pdb=" N ALA B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 Processing helix chain 'B' and resid 527 through 536 removed outlier: 3.575A pdb=" N GLN B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 554 removed outlier: 3.790A pdb=" N LEU B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.605A pdb=" N VAL B 587 " --> pdb=" O TYR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 608 removed outlier: 5.146A pdb=" N ILE B 597 " --> pdb=" O PRO B 593 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 4.004A pdb=" N ALA B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 4.251A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 80 removed outlier: 4.021A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 4.090A pdb=" N GLN C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.943A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 130 removed outlier: 3.618A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.711A pdb=" N ILE C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 193 removed outlier: 4.248A pdb=" N LYS C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLN C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.760A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 205 through 208 removed outlier: 3.827A pdb=" N GLU C 208 " --> pdb=" O GLY C 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 205 through 208' Processing helix chain 'C' and resid 220 through 230 removed outlier: 4.064A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.534A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 293 through 299 removed outlier: 3.968A pdb=" N VAL C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.697A pdb=" N GLU C 312 " --> pdb=" O PHE C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 366 through 383 removed outlier: 4.088A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 378 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.915A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 411 removed outlier: 3.854A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 4.478A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.601A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 449 through 464 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.640A pdb=" N ARG C 482 " --> pdb=" O TRP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 505 through 509 removed outlier: 3.578A pdb=" N ASN C 508 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP C 509 " --> pdb=" O VAL C 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 505 through 509' Processing helix chain 'C' and resid 513 through 534 removed outlier: 3.900A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.731A pdb=" N LYS C 541 " --> pdb=" O PRO C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.820A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 559 " --> pdb=" O PHE C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.577A pdb=" N LEU C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.752A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.619A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 3.644A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 642 " --> pdb=" O ASN C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 716 removed outlier: 3.618A pdb=" N VAL C 700 " --> pdb=" O PRO C 696 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 705 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 767 removed outlier: 4.081A pdb=" N ILE C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL C 752 " --> pdb=" O VAL C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 27 through 31 removed outlier: 4.076A pdb=" N SER D 30 " --> pdb=" O GLU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.589A pdb=" N CYS D 49 " --> pdb=" O CYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 64 removed outlier: 4.066A pdb=" N TYR D 60 " --> pdb=" O TRP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 81 Processing helix chain 'D' and resid 82 through 96 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 142 removed outlier: 3.959A pdb=" N GLY D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR D 128 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 194 through 212 removed outlier: 3.886A pdb=" N LEU D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS D 200 " --> pdb=" O TRP D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 3.691A pdb=" N ALA D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 242 removed outlier: 3.935A pdb=" N THR D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 removed outlier: 4.203A pdb=" N THR D 256 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 279 removed outlier: 3.830A pdb=" N TRP D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D 279 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 299 through 349 Processing helix chain 'D' and resid 359 through 371 Processing helix chain 'D' and resid 371 through 377 Processing helix chain 'D' and resid 402 through 408 Processing helix chain 'D' and resid 412 through 446 removed outlier: 3.505A pdb=" N TRP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY D 434 " --> pdb=" O SER D 430 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL D 439 " --> pdb=" O ASN D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 454 through 470 removed outlier: 3.940A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 removed outlier: 3.543A pdb=" N LEU D 475 " --> pdb=" O ILE D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 490 removed outlier: 3.658A pdb=" N TRP D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY D 490 " --> pdb=" O ASP D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 508 removed outlier: 4.488A pdb=" N ALA D 498 " --> pdb=" O LEU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 523 Processing helix chain 'D' and resid 527 through 536 removed outlier: 3.575A pdb=" N GLN D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 554 removed outlier: 3.789A pdb=" N LEU D 540 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE D 550 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 554 " --> pdb=" O PHE D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 582 through 591 removed outlier: 3.605A pdb=" N VAL D 587 " --> pdb=" O TYR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 608 removed outlier: 5.145A pdb=" N ILE D 597 " --> pdb=" O PRO D 593 " (cutoff:3.500A) Proline residue: D 598 - end of helix removed outlier: 4.004A pdb=" N ALA D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.906A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.701A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 673 removed outlier: 6.434A pdb=" N ASP A 693 " --> pdb=" O ALA A 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AA6, first strand: chain 'B' and resid 559 through 562 Processing sheet with id=AA7, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AA8, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.906A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.700A pdb=" N LEU C 351 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 670 through 673 removed outlier: 6.434A pdb=" N ASP C 693 " --> pdb=" O ALA C 687 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 670 through 673 Processing sheet with id=AB3, first strand: chain 'D' and resid 559 through 562 1091 hydrogen bonds defined for protein. 3189 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: 7.07 Time building geometry restraints manager: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6824 1.34 - 1.46: 6109 1.46 - 1.59: 9805 1.59 - 1.71: 0 1.71 - 1.84: 210 Bond restraints: 22948 Sorted by residual: bond pdb=" CA GLU A 467 " pdb=" C GLU A 467 " ideal model delta sigma weight residual 1.522 1.464 0.058 1.72e-02 3.38e+03 1.13e+01 bond pdb=" CA GLU C 467 " pdb=" C GLU C 467 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.72e-02 3.38e+03 1.10e+01 bond pdb=" CA ALA A 193 " pdb=" C ALA A 193 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.80e-02 3.09e+03 9.73e+00 bond pdb=" CA ALA C 193 " pdb=" C ALA C 193 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.80e-02 3.09e+03 9.73e+00 bond pdb=" C SER C 611 " pdb=" N PRO C 612 " ideal model delta sigma weight residual 1.335 1.299 0.036 1.19e-02 7.06e+03 9.11e+00 ... (remaining 22943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 29365 1.83 - 3.67: 1639 3.67 - 5.50: 178 5.50 - 7.33: 48 7.33 - 9.16: 6 Bond angle restraints: 31236 Sorted by residual: angle pdb=" N GLU A 87 " pdb=" CA GLU A 87 " pdb=" C GLU A 87 " ideal model delta sigma weight residual 114.56 106.98 7.58 1.27e+00 6.20e-01 3.56e+01 angle pdb=" N GLU C 87 " pdb=" CA GLU C 87 " pdb=" C GLU C 87 " ideal model delta sigma weight residual 114.56 107.05 7.51 1.27e+00 6.20e-01 3.50e+01 angle pdb=" N GLU D 352 " pdb=" CA GLU D 352 " pdb=" C GLU D 352 " ideal model delta sigma weight residual 111.07 116.63 -5.56 1.07e+00 8.73e-01 2.70e+01 angle pdb=" N GLU B 352 " pdb=" CA GLU B 352 " pdb=" C GLU B 352 " ideal model delta sigma weight residual 111.07 116.60 -5.53 1.07e+00 8.73e-01 2.67e+01 angle pdb=" N VAL D 55 " pdb=" CA VAL D 55 " pdb=" C VAL D 55 " ideal model delta sigma weight residual 112.96 108.19 4.77 1.00e+00 1.00e+00 2.27e+01 ... (remaining 31231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12217 17.98 - 35.96: 1236 35.96 - 53.95: 380 53.95 - 71.93: 83 71.93 - 89.91: 32 Dihedral angle restraints: 13948 sinusoidal: 6038 harmonic: 7910 Sorted by residual: dihedral pdb=" CA THR C 730 " pdb=" C THR C 730 " pdb=" N LEU C 731 " pdb=" CA LEU C 731 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA THR A 730 " pdb=" C THR A 730 " pdb=" N LEU A 731 " pdb=" CA LEU A 731 " ideal model delta harmonic sigma weight residual -180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CB CYS D 336 " pdb=" SG CYS D 336 " pdb=" SG CYS D 383 " pdb=" CB CYS D 383 " ideal model delta sinusoidal sigma weight residual -86.00 -131.02 45.02 1 1.00e+01 1.00e-02 2.81e+01 ... (remaining 13945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2404 0.054 - 0.109: 960 0.109 - 0.163: 138 0.163 - 0.217: 19 0.217 - 0.272: 7 Chirality restraints: 3528 Sorted by residual: chirality pdb=" CA ILE C 727 " pdb=" N ILE C 727 " pdb=" C ILE C 727 " pdb=" CB ILE C 727 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE A 727 " pdb=" N ILE A 727 " pdb=" C ILE A 727 " pdb=" CB ILE A 727 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3525 not shown) Planarity restraints: 3938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 676 " 0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO C 677 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 677 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 677 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 676 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A 677 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 677 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 677 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 687 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 688 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 688 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 688 " -0.028 5.00e-02 4.00e+02 ... (remaining 3935 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 107 2.45 - 3.07: 16162 3.07 - 3.68: 31668 3.68 - 4.29: 47942 4.29 - 4.90: 80606 Nonbonded interactions: 176485 Sorted by model distance: nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.843 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.843 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 902 " model vdw 2.009 2.230 nonbonded pdb=" OE1 GLU C 402 " pdb="ZN ZN C 902 " model vdw 2.009 2.230 nonbonded pdb=" N ASP C 367 " pdb=" OD1 ASP C 367 " model vdw 2.155 3.120 ... (remaining 176480 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 52.080 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 : 0.013 0.076 22948 Z= 0.821 Angle : 0.934 9.163 31236 Z= 0.543 Chirality : 0.055 0.272 3528 Planarity : 0.005 0.087 3914 Dihedral : 16.448 89.908 8830 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.89 % Favored : 91.89 % Rotamer: Outliers : 5.36 % Allowed : 13.26 % Favored : 81.38 % 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: -3.72 (0.13), residues: 2700 helix: -1.90 (0.11), residues: 1544 sheet: -1.41 (0.72), residues: 42 loop : -3.29 (0.16), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 566 HIS 0.008 0.002 HIS C 241 PHE 0.014 0.002 PHE D 549 TYR 0.027 0.002 TYR C 385 ARG 0.004 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 286 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8664 (m-40) REVERT: A 735 ASN cc_start: 0.6752 (OUTLIER) cc_final: 0.6354 (p0) REVERT: A 766 ARG cc_start: 0.4643 (OUTLIER) cc_final: 0.3997 (ttt180) REVERT: C 290 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8649 (m-40) REVERT: C 735 ASN cc_start: 0.6743 (OUTLIER) cc_final: 0.6341 (p0) REVERT: C 766 ARG cc_start: 0.4808 (OUTLIER) cc_final: 0.4132 (ttt180) outliers start: 128 outliers final: 38 residues processed: 406 average time/residue: 0.3117 time to fit residues: 203.3787 Evaluate side-chains 196 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 152 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 ASN Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 766 ARG Chi-restraints excluded: chain D residue 129 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 0.0270 chunk 210 optimal weight: 0.0040 chunk 81 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 overall best weight: 0.5450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 63 ASN A 101 GLN A 239 HIS A 250 ASN A 277 ASN A 373 HIS A 493 HIS A 556 ASN A 586 ASN A 599 ASN A 682 ASN A 735 ASN B 194 GLN B 435 ASN B 444 GLN C 33 ASN C 63 ASN C 101 GLN C 239 HIS C 250 ASN C 277 ASN C 373 HIS C 493 HIS C 556 ASN C 586 ASN C 599 ASN C 682 ASN C 735 ASN D 194 GLN D 435 ASN D 444 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22948 Z= 0.183 Angle : 0.687 12.711 31236 Z= 0.346 Chirality : 0.044 0.333 3528 Planarity : 0.004 0.051 3914 Dihedral : 8.735 82.923 3798 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 3.77 % Allowed : 16.49 % Favored : 79.75 % 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: -1.78 (0.15), residues: 2700 helix: -0.31 (0.13), residues: 1594 sheet: -1.49 (0.60), residues: 62 loop : -2.52 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 104 HIS 0.005 0.001 HIS D 65 PHE 0.020 0.001 PHE B 283 TYR 0.018 0.001 TYR D 567 ARG 0.004 0.000 ARG C 768 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 190 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.6603 (OUTLIER) cc_final: 0.6370 (m90) REVERT: A 297 MET cc_start: 0.8202 (ttm) cc_final: 0.7896 (mtp) REVERT: A 596 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8575 (mtmt) REVERT: A 766 ARG cc_start: 0.4271 (OUTLIER) cc_final: 0.3520 (ttt180) REVERT: C 297 MET cc_start: 0.8200 (ttm) cc_final: 0.7890 (mtp) REVERT: C 596 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8570 (mtmt) REVERT: C 735 ASN cc_start: 0.6172 (OUTLIER) cc_final: 0.5959 (p0) REVERT: C 766 ARG cc_start: 0.4392 (OUTLIER) cc_final: 0.3629 (ttt180) outliers start: 90 outliers final: 33 residues processed: 273 average time/residue: 0.3422 time to fit residues: 153.4374 Evaluate side-chains 175 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 ASN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LYS Chi-restraints excluded: chain D residue 536 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 64.1312 > 50: distance: 28 - 45: 6.206 distance: 32 - 54: 13.360 distance: 36 - 65: 31.929 distance: 43 - 45: 4.707 distance: 45 - 46: 13.109 distance: 46 - 47: 18.422 distance: 46 - 49: 10.053 distance: 47 - 48: 16.078 distance: 47 - 54: 20.833 distance: 50 - 51: 3.034 distance: 51 - 52: 3.077 distance: 51 - 53: 6.928 distance: 54 - 55: 20.980 distance: 55 - 56: 47.164 distance: 55 - 58: 20.453 distance: 56 - 57: 33.079 distance: 56 - 65: 64.131 distance: 58 - 59: 6.069 distance: 59 - 60: 9.655 distance: 60 - 61: 3.912 distance: 61 - 62: 7.031 distance: 62 - 63: 7.044 distance: 62 - 64: 3.012 distance: 65 - 66: 62.148 distance: 66 - 67: 48.607 distance: 66 - 69: 31.916 distance: 67 - 68: 37.081 distance: 67 - 73: 43.793 distance: 69 - 70: 35.926 distance: 70 - 71: 19.382 distance: 70 - 72: 18.510 distance: 73 - 74: 33.542 distance: 74 - 75: 25.845 distance: 74 - 77: 10.868 distance: 75 - 76: 18.198 distance: 75 - 84: 26.099 distance: 77 - 78: 5.234 distance: 78 - 79: 3.952 distance: 79 - 80: 5.407 distance: 80 - 81: 8.491 distance: 81 - 82: 3.992 distance: 81 - 83: 6.638 distance: 84 - 85: 15.668 distance: 85 - 86: 16.442 distance: 85 - 88: 3.282 distance: 86 - 87: 27.610 distance: 86 - 95: 18.045 distance: 88 - 89: 5.868 distance: 89 - 90: 4.035 distance: 90 - 91: 4.376 distance: 92 - 93: 3.749 distance: 92 - 94: 4.277 distance: 95 - 96: 21.037 distance: 96 - 97: 29.393 distance: 97 - 98: 33.332 distance: 97 - 99: 27.472 distance: 99 - 100: 17.410 distance: 100 - 101: 11.671 distance: 100 - 103: 15.928 distance: 101 - 102: 12.423 distance: 101 - 105: 16.778 distance: 103 - 104: 17.230 distance: 105 - 106: 15.265 distance: 106 - 107: 18.312 distance: 106 - 109: 8.181 distance: 107 - 108: 17.794 distance: 107 - 113: 17.085 distance: 108 - 138: 9.998 distance: 109 - 110: 3.468 distance: 110 - 111: 4.950 distance: 110 - 112: 8.469 distance: 113 - 114: 18.154 distance: 114 - 115: 42.753 distance: 115 - 116: 38.149 distance: 115 - 117: 41.220 distance: 116 - 144: 11.206 distance: 117 - 118: 14.353 distance: 118 - 119: 18.327 distance: 118 - 121: 14.063 distance: 119 - 120: 18.926 distance: 119 - 124: 11.875 distance: 121 - 122: 5.251 distance: 121 - 123: 9.695 distance: 155 - 161: 3.016