Starting phenix.real_space_refine on Wed Jun 18 23:24:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i91_35254/06_2025/8i91_35254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i91_35254/06_2025/8i91_35254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i91_35254/06_2025/8i91_35254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i91_35254/06_2025/8i91_35254.map" model { file = "/net/cci-nas-00/data/ceres_data/8i91_35254/06_2025/8i91_35254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i91_35254/06_2025/8i91_35254.cif" } resolution = 3.3 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= 0.007 sd= 0.117 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 130 5.16 5 Cl 2 4.86 5 C 14100 2.51 5 N 3486 2.21 5 O 4044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21764 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: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4552 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 557} 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: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4552 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 557} 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 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: "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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 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 Time building chain proxies: 13.31, per 1000 atoms: 0.61 Number of scatterers: 21764 At special positions: 0 Unit cell: (122.831, 138.049, 179.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 130 16.00 O 4044 8.00 N 3486 7.00 C 14100 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=2.05 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 126 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 358 " 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 126 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 358 " 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 Number of custom bonds: simple=0, 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 703 " - " ASN B 131 " " NAG C 901 " - " ASN C 322 " " NAG D 703 " - " ASN D 131 " " 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 357 " " 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 357 " Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 2.9 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 " 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4992 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 12 sheets defined 65.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.593A pdb=" N ASP A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.850A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.684A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.992A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.566A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.535A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.591A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 3.751A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.761A 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 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.908A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.614A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) 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 305 through 319 removed outlier: 3.528A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.030A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.699A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.606A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.729A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.630A 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: 3.816A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.648A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 3.663A 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 531 removed outlier: 3.988A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.593A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 4.313A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.520A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.818A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.612A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 removed outlier: 3.517A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 715 removed outlier: 3.565A pdb=" N VAL A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 767 removed outlier: 3.513A pdb=" N VAL A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.971A pdb=" N VAL B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.203A pdb=" N VAL B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 29' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.640A pdb=" N TYR B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.622A pdb=" N LEU B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 55 through 69 removed outlier: 3.688A pdb=" N LEU B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.635A pdb=" N THR B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 84 Processing helix chain 'B' and resid 85 through 116 removed outlier: 4.203A pdb=" N VAL B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.613A pdb=" N LYS B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 168 through 185 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 192 through 202 removed outlier: 4.118A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.664A pdb=" N TRP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 272 through 320 removed outlier: 4.193A pdb=" N ILE B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.622A pdb=" N GLU B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.628A pdb=" N SER B 349 " --> pdb=" O PRO B 345 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.680A pdb=" N GLU B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 416 removed outlier: 3.663A pdb=" N TRP B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.525A pdb=" N SER B 426 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 427' Processing helix chain 'B' and resid 431 through 445 removed outlier: 3.629A pdb=" N GLY B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.885A pdb=" N TRP B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 483 removed outlier: 3.828A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 512 through 532 removed outlier: 4.356A pdb=" N ASP B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 3.594A pdb=" N LEU B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 removed outlier: 3.921A pdb=" N LEU B 572 " --> pdb=" O MET B 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 3.597A pdb=" N ASP C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 80 removed outlier: 3.850A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.684A pdb=" N GLN C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.992A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 130 removed outlier: 3.566A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.535A pdb=" N MET C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.592A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 193 Proline residue: C 178 - end of helix removed outlier: 3.751A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.761A 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 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.907A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.615A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) 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 305 through 319 removed outlier: 3.528A pdb=" N GLY C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 366 through 383 removed outlier: 4.030A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.699A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 410 removed outlier: 3.606A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 4.728A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.630A 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: 3.817A pdb=" N ARG C 482 " --> pdb=" O TRP C 478 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 505 through 509 removed outlier: 3.648A pdb=" N ASN C 508 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 3.663A 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 531 removed outlier: 3.988A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.593A pdb=" N LYS C 541 " --> pdb=" O PRO C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 4.312A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.521A pdb=" N LEU C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.818A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.612A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 removed outlier: 3.518A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 656 " --> pdb=" O ARG C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 696 through 715 removed outlier: 3.566A pdb=" N VAL C 700 " --> pdb=" O PRO C 696 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 705 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 767 removed outlier: 3.513A pdb=" N VAL C 752 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE C 761 " --> pdb=" O ILE C 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.971A pdb=" N VAL D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.203A pdb=" N VAL D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 29' Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.639A pdb=" N TYR D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.621A pdb=" N LEU D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.688A pdb=" N LEU D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.635A pdb=" N THR D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 84 Processing helix chain 'D' and resid 85 through 116 removed outlier: 4.202A pdb=" N VAL D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 removed outlier: 3.613A pdb=" N LYS D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 168 through 185 Processing helix chain 'D' and resid 188 through 191 Processing helix chain 'D' and resid 192 through 202 removed outlier: 4.118A pdb=" N ALA D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER D 201 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.664A pdb=" N TRP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 272 through 320 removed outlier: 4.192A pdb=" N ILE D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL D 313 " --> pdb=" O CYS D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 340 removed outlier: 3.622A pdb=" N GLU D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.628A pdb=" N SER D 349 " --> pdb=" O PRO D 345 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.680A pdb=" N GLU D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 416 removed outlier: 3.663A pdb=" N TRP D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.525A pdb=" N SER D 426 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 423 through 427' Processing helix chain 'D' and resid 431 through 445 removed outlier: 3.630A pdb=" N GLY D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.885A pdb=" N TRP D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 483 removed outlier: 3.828A pdb=" N LEU D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 477 " --> pdb=" O VAL D 473 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR D 482 " --> pdb=" O ILE D 478 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 491 Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 512 through 532 removed outlier: 4.356A pdb=" N ASP D 527 " --> pdb=" O PHE D 523 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU D 530 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY D 532 " --> pdb=" O TYR D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 3.595A pdb=" N LEU D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.920A pdb=" N LEU D 572 " --> pdb=" O MET D 568 " (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: 5.923A 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: 3.726A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 6.313A 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: 6.731A 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 535 through 538 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: 5.924A 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: 3.727A pdb=" N LEU C 351 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 6.314A 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: 6.731A 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 535 through 538 1045 hydrogen bonds defined for protein. 3045 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: 6.31 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6807 1.35 - 1.48: 6383 1.48 - 1.62: 8932 1.62 - 1.75: 0 1.75 - 1.88: 216 Bond restraints: 22338 Sorted by residual: bond pdb=" CA THR B 192 " pdb=" C THR B 192 " ideal model delta sigma weight residual 1.523 1.583 -0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" CA THR D 192 " pdb=" C THR D 192 " ideal model delta sigma weight residual 1.523 1.583 -0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" N PRO C 677 " pdb=" CD PRO C 677 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.86e+01 bond pdb=" N PRO A 677 " pdb=" CD PRO A 677 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" N THR B 192 " pdb=" CA THR B 192 " ideal model delta sigma weight residual 1.457 1.512 -0.055 1.29e-02 6.01e+03 1.80e+01 ... (remaining 22333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 29581 2.70 - 5.40: 709 5.40 - 8.10: 80 8.10 - 10.80: 4 10.80 - 13.50: 8 Bond angle restraints: 30382 Sorted by residual: angle pdb=" N GLY B 193 " pdb=" CA GLY B 193 " pdb=" C GLY B 193 " ideal model delta sigma weight residual 112.64 118.43 -5.79 1.21e+00 6.83e-01 2.29e+01 angle pdb=" N GLY D 193 " pdb=" CA GLY D 193 " pdb=" C GLY D 193 " ideal model delta sigma weight residual 112.64 118.43 -5.79 1.21e+00 6.83e-01 2.29e+01 angle pdb=" C VAL D 45 " pdb=" N PRO D 46 " pdb=" CA PRO D 46 " ideal model delta sigma weight residual 119.05 113.78 5.27 1.11e+00 8.12e-01 2.25e+01 angle pdb=" C VAL B 45 " pdb=" N PRO B 46 " pdb=" CA PRO B 46 " ideal model delta sigma weight residual 119.05 113.78 5.27 1.11e+00 8.12e-01 2.25e+01 angle pdb=" C PHE D 228 " pdb=" N THR D 229 " pdb=" CA THR D 229 " ideal model delta sigma weight residual 120.49 113.77 6.72 1.42e+00 4.96e-01 2.24e+01 ... (remaining 30377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 11637 17.75 - 35.50: 1339 35.50 - 53.25: 408 53.25 - 71.00: 96 71.00 - 88.75: 38 Dihedral angle restraints: 13518 sinusoidal: 5740 harmonic: 7778 Sorted by residual: dihedral pdb=" CA ALA D 500 " pdb=" C ALA D 500 " pdb=" N VAL D 501 " pdb=" CA VAL D 501 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ALA B 500 " pdb=" C ALA B 500 " pdb=" N VAL B 501 " pdb=" CA VAL B 501 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 46.42 46.58 1 1.00e+01 1.00e-02 3.00e+01 ... (remaining 13515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 3396 0.186 - 0.373: 24 0.373 - 0.559: 0 0.559 - 0.746: 0 0.746 - 0.932: 2 Chirality restraints: 3422 Sorted by residual: chirality pdb=" C1 NAG D 703 " pdb=" ND2 ASN D 131 " pdb=" C2 NAG D 703 " pdb=" O5 NAG D 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 131 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" CA TYR D 463 " pdb=" N TYR D 463 " pdb=" C TYR D 463 " pdb=" CB TYR D 463 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3419 not shown) Planarity restraints: 3808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 131 " 0.022 2.00e-02 2.50e+03 4.56e-02 2.59e+01 pdb=" CG ASN B 131 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 131 " 0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN B 131 " -0.081 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 131 " -0.022 2.00e-02 2.50e+03 4.56e-02 2.59e+01 pdb=" CG ASN D 131 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN D 131 " -0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN D 131 " 0.081 2.00e-02 2.50e+03 pdb=" C1 NAG D 703 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 732 " -0.063 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO A 733 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 733 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 733 " -0.051 5.00e-02 4.00e+02 ... (remaining 3805 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 144 2.45 - 3.06: 16119 3.06 - 3.67: 30575 3.67 - 4.29: 45658 4.29 - 4.90: 76502 Nonbonded interactions: 168998 Sorted by model distance: nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.837 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.837 2.230 nonbonded pdb=" O TYR B 265 " pdb=" O ASN B 266 " model vdw 1.948 3.040 nonbonded pdb=" O TYR D 265 " pdb=" O ASN D 266 " model vdw 1.948 3.040 nonbonded pdb=" O GLY D 485 " pdb=" N ARG D 487 " model vdw 2.027 3.120 ... (remaining 168993 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: 0.05 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: 1.580 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: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 52.450 Find NCS groups from input model: 0.860 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5054 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 : 0.011 0.308 22384 Z= 0.515 Angle : 1.122 50.722 30498 Z= 0.619 Chirality : 0.062 0.932 3422 Planarity : 0.005 0.096 3790 Dihedral : 17.225 88.753 8496 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 2.15 % Allowed : 12.88 % Favored : 84.97 % Rotamer: Outliers : 8.31 % Allowed : 15.93 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -4.52 (0.13), residues: 2648 helix: -2.56 (0.10), residues: 1562 sheet: -2.13 (0.57), residues: 68 loop : -3.64 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 509 HIS 0.007 0.002 HIS C 417 PHE 0.014 0.002 PHE A 274 TYR 0.022 0.002 TYR C 183 ARG 0.020 0.001 ARG D 582 Details of bonding type rmsd link_NAG-ASN : bond 0.01452 ( 18) link_NAG-ASN : angle 10.41391 ( 54) link_BETA1-4 : bond 0.00645 ( 14) link_BETA1-4 : angle 2.34888 ( 42) hydrogen bonds : bond 0.18524 ( 1037) hydrogen bonds : angle 7.54924 ( 3045) metal coordination : bond 0.24273 ( 4) SS BOND : bond 0.00850 ( 10) SS BOND : angle 3.34300 ( 20) covalent geometry : bond 0.01081 (22338) covalent geometry : angle 1.02707 (30382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 556 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8063 (mp10) cc_final: 0.7744 (pm20) REVERT: A 154 ASN cc_start: 0.7847 (m110) cc_final: 0.7589 (m-40) REVERT: A 190 MET cc_start: 0.7952 (tmt) cc_final: 0.7605 (tmm) REVERT: A 199 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.5261 (t80) REVERT: A 210 ASN cc_start: 0.8639 (m-40) cc_final: 0.8189 (m-40) REVERT: A 276 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 309 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7831 (mmtp) REVERT: A 330 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7829 (p0) REVERT: A 350 ASP cc_start: 0.5858 (t0) cc_final: 0.5542 (t70) REVERT: A 470 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7480 (ttmt) REVERT: A 559 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7445 (ptm-80) REVERT: A 568 LEU cc_start: 0.8230 (tp) cc_final: 0.7968 (tt) REVERT: A 572 ASN cc_start: 0.8587 (m-40) cc_final: 0.8246 (m-40) REVERT: A 577 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8033 (mtmm) REVERT: A 601 ASN cc_start: 0.7091 (m-40) cc_final: 0.6883 (p0) REVERT: A 640 MET cc_start: 0.7358 (mmm) cc_final: 0.7113 (mmm) REVERT: A 651 MET cc_start: 0.7745 (mmm) cc_final: 0.7482 (mmm) REVERT: A 662 MET cc_start: 0.6406 (tpt) cc_final: 0.5961 (tpp) REVERT: A 760 LEU cc_start: 0.2040 (OUTLIER) cc_final: 0.1809 (tt) REVERT: B 101 TYR cc_start: 0.7121 (p90) cc_final: 0.6561 (p90) REVERT: B 136 ASP cc_start: 0.6947 (t0) cc_final: 0.6457 (p0) REVERT: B 324 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5550 (pm20) REVERT: B 333 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.2853 (tp) REVERT: B 359 SER cc_start: 0.7524 (t) cc_final: 0.7181 (p) REVERT: B 380 GLU cc_start: 0.4954 (mm-30) cc_final: 0.4054 (mm-30) REVERT: B 406 SER cc_start: 0.6705 (OUTLIER) cc_final: 0.6486 (p) REVERT: B 473 VAL cc_start: 0.7218 (t) cc_final: 0.6929 (t) REVERT: C 113 SER cc_start: 0.7095 (OUTLIER) cc_final: 0.6771 (p) REVERT: C 156 LEU cc_start: 0.8465 (mt) cc_final: 0.8191 (tp) REVERT: C 182 GLU cc_start: 0.5355 (tt0) cc_final: 0.5081 (mt-10) REVERT: C 330 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7825 (p0) REVERT: C 366 MET cc_start: 0.8051 (ttt) cc_final: 0.7823 (ttm) REVERT: C 383 MET cc_start: 0.8245 (mtp) cc_final: 0.8022 (mtt) REVERT: C 408 MET cc_start: 0.8599 (mpp) cc_final: 0.8319 (mmm) REVERT: C 416 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8338 (ttpt) REVERT: C 625 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7708 (mttt) REVERT: C 637 ASP cc_start: 0.7164 (m-30) cc_final: 0.6865 (m-30) REVERT: C 667 GLU cc_start: 0.5884 (pp20) cc_final: 0.5174 (mp0) REVERT: C 668 GLU cc_start: 0.7702 (pm20) cc_final: 0.7367 (pm20) REVERT: C 669 ASP cc_start: 0.6895 (m-30) cc_final: 0.6668 (m-30) REVERT: C 740 SER cc_start: 0.1268 (OUTLIER) cc_final: 0.1064 (m) REVERT: D 38 TYR cc_start: 0.3966 (m-80) cc_final: 0.3173 (m-80) REVERT: D 187 ARG cc_start: 0.3551 (OUTLIER) cc_final: 0.3339 (mtt180) REVERT: D 281 LEU cc_start: 0.7763 (mt) cc_final: 0.7522 (tp) REVERT: D 324 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5665 (mm-30) REVERT: D 334 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: D 344 TYR cc_start: 0.7544 (m-80) cc_final: 0.6777 (m-80) outliers start: 192 outliers final: 38 residues processed: 707 average time/residue: 0.3299 time to fit residues: 358.7754 Evaluate side-chains 391 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 335 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN A 149 ASN A 154 ASN A 250 ASN A 345 HIS A 493 HIS A 505 HIS A 556 ASN A 586 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 736 GLN B 118 GLN B 273 GLN B 275 HIS B 283 ASN B 410 ASN B 537 GLN C 33 ASN C 42 GLN C 63 ASN C 149 ASN C 154 ASN C 239 HIS C 250 ASN C 345 HIS C 493 HIS C 505 HIS C 556 ASN C 586 ASN C 599 ASN C 682 ASN C 736 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 243 ASN D 273 GLN D 283 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.244846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.223407 restraints weight = 26022.770| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 1.13 r_work: 0.4271 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.4241 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22384 Z= 0.188 Angle : 0.773 10.748 30498 Z= 0.387 Chirality : 0.049 0.636 3422 Planarity : 0.005 0.101 3790 Dihedral : 9.013 86.144 3639 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.19 % Favored : 91.58 % Rotamer: Outliers : 4.29 % Allowed : 19.31 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.43 (0.15), residues: 2648 helix: -0.78 (0.12), residues: 1582 sheet: -1.63 (0.55), residues: 82 loop : -2.95 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 509 HIS 0.010 0.001 HIS D 132 PHE 0.025 0.002 PHE A 746 TYR 0.028 0.002 TYR B 210 ARG 0.008 0.001 ARG A 766 Details of bonding type rmsd link_NAG-ASN : bond 0.02021 ( 18) link_NAG-ASN : angle 2.65901 ( 54) link_BETA1-4 : bond 0.00634 ( 14) link_BETA1-4 : angle 1.80267 ( 42) hydrogen bonds : bond 0.06283 ( 1037) hydrogen bonds : angle 4.97497 ( 3045) metal coordination : bond 0.01396 ( 4) SS BOND : bond 0.00794 ( 10) SS BOND : angle 2.72923 ( 20) covalent geometry : bond 0.00403 (22338) covalent geometry : angle 0.75974 (30382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 357 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8103 (m-40) cc_final: 0.7879 (m-40) REVERT: A 228 HIS cc_start: 0.7504 (t70) cc_final: 0.7124 (m170) REVERT: A 276 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8556 (p) REVERT: A 282 THR cc_start: 0.7489 (p) cc_final: 0.7191 (p) REVERT: A 768 ARG cc_start: -0.0495 (OUTLIER) cc_final: -0.2434 (mmp-170) REVERT: B 101 TYR cc_start: 0.6621 (p90) cc_final: 0.6338 (p90) REVERT: C 474 MET cc_start: 0.7853 (mmp) cc_final: 0.7631 (mmp) REVERT: C 662 MET cc_start: 0.7859 (tpp) cc_final: 0.7507 (tpt) REVERT: C 740 SER cc_start: 0.3474 (OUTLIER) cc_final: 0.3094 (m) REVERT: D 69 MET cc_start: 0.5891 (mmt) cc_final: 0.5550 (mmt) REVERT: D 139 CYS cc_start: 0.3851 (OUTLIER) cc_final: 0.3446 (t) REVERT: D 149 TRP cc_start: 0.5841 (t60) cc_final: 0.5523 (t-100) REVERT: D 398 MET cc_start: 0.6571 (tmm) cc_final: 0.6270 (tmm) outliers start: 99 outliers final: 41 residues processed: 439 average time/residue: 0.2853 time to fit residues: 203.3081 Evaluate side-chains 321 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 276 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 205 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 ASN A 340 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 270 ASN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.239981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.215127 restraints weight = 25824.164| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 1.32 r_work: 0.4115 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4086 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22384 Z= 0.166 Angle : 0.692 11.389 30498 Z= 0.344 Chirality : 0.045 0.336 3422 Planarity : 0.005 0.086 3790 Dihedral : 6.859 59.647 3577 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.33 % Favored : 92.41 % Rotamer: Outliers : 3.90 % Allowed : 19.78 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.58 (0.16), residues: 2648 helix: -0.15 (0.13), residues: 1608 sheet: -1.64 (0.54), residues: 70 loop : -2.49 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 168 HIS 0.007 0.001 HIS C 241 PHE 0.025 0.002 PHE B 110 TYR 0.018 0.001 TYR B 38 ARG 0.006 0.001 ARG B 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00939 ( 18) link_NAG-ASN : angle 3.18138 ( 54) link_BETA1-4 : bond 0.00418 ( 14) link_BETA1-4 : angle 1.91582 ( 42) hydrogen bonds : bond 0.05308 ( 1037) hydrogen bonds : angle 4.51334 ( 3045) metal coordination : bond 0.00420 ( 4) SS BOND : bond 0.00974 ( 10) SS BOND : angle 1.92706 ( 20) covalent geometry : bond 0.00369 (22338) covalent geometry : angle 0.67455 (30382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 289 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 HIS cc_start: 0.7671 (t70) cc_final: 0.7375 (m170) REVERT: A 340 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7041 (tp40) REVERT: A 479 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7477 (mt-10) REVERT: A 768 ARG cc_start: -0.0780 (OUTLIER) cc_final: -0.4010 (mpp80) REVERT: B 101 TYR cc_start: 0.6922 (p90) cc_final: 0.6586 (p90) REVERT: C 401 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7556 (t-90) REVERT: C 471 ASP cc_start: 0.7727 (t0) cc_final: 0.7454 (t0) REVERT: C 495 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7611 (mm-30) REVERT: C 662 MET cc_start: 0.7991 (tpp) cc_final: 0.7687 (tpt) REVERT: D 69 MET cc_start: 0.5749 (mmt) cc_final: 0.5536 (mmt) REVERT: D 139 CYS cc_start: 0.3824 (OUTLIER) cc_final: 0.3413 (t) outliers start: 90 outliers final: 44 residues processed: 357 average time/residue: 0.2797 time to fit residues: 163.5151 Evaluate side-chains 292 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 570 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 58 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN C 64 ASN D 67 GLN D 115 HIS D 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.234227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.205876 restraints weight = 25489.670| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 1.50 r_work: 0.3558 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22384 Z= 0.183 Angle : 0.686 11.750 30498 Z= 0.339 Chirality : 0.045 0.290 3422 Planarity : 0.005 0.074 3790 Dihedral : 6.466 58.517 3569 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.99 % Favored : 92.79 % Rotamer: Outliers : 3.07 % Allowed : 20.87 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.33 (0.16), residues: 2648 helix: -0.01 (0.13), residues: 1628 sheet: -1.48 (0.55), residues: 70 loop : -2.33 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 149 HIS 0.008 0.001 HIS A 241 PHE 0.028 0.002 PHE D 457 TYR 0.022 0.002 TYR B 38 ARG 0.004 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00787 ( 18) link_NAG-ASN : angle 2.99402 ( 54) link_BETA1-4 : bond 0.00389 ( 14) link_BETA1-4 : angle 1.84188 ( 42) hydrogen bonds : bond 0.05096 ( 1037) hydrogen bonds : angle 4.41795 ( 3045) metal coordination : bond 0.00448 ( 4) SS BOND : bond 0.00890 ( 10) SS BOND : angle 2.35357 ( 20) covalent geometry : bond 0.00431 (22338) covalent geometry : angle 0.66917 (30382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 260 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8182 (t0) cc_final: 0.7959 (t0) REVERT: A 332 MET cc_start: 0.8523 (tpp) cc_final: 0.8240 (tpp) REVERT: A 479 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 768 ARG cc_start: -0.1589 (OUTLIER) cc_final: -0.3967 (mpp80) REVERT: B 446 MET cc_start: 0.7079 (mmm) cc_final: 0.6753 (mmm) REVERT: C 480 MET cc_start: 0.9135 (mtp) cc_final: 0.8900 (mtm) REVERT: C 495 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7855 (mm-30) REVERT: C 662 MET cc_start: 0.7824 (tpp) cc_final: 0.7540 (tpt) REVERT: C 667 GLU cc_start: 0.7107 (mp0) cc_final: 0.6720 (mp0) REVERT: C 750 MET cc_start: 0.3895 (ptt) cc_final: 0.3664 (ptp) REVERT: D 139 CYS cc_start: 0.4502 (OUTLIER) cc_final: 0.3953 (t) REVERT: D 205 CYS cc_start: 0.5243 (OUTLIER) cc_final: 0.4514 (m) REVERT: D 275 HIS cc_start: 0.4579 (OUTLIER) cc_final: 0.4325 (m-70) outliers start: 71 outliers final: 49 residues processed: 312 average time/residue: 0.2830 time to fit residues: 143.8912 Evaluate side-chains 290 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 570 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 104 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 185 optimal weight: 0.2980 chunk 115 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN C 24 GLN D 218 HIS D 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.234151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.191810 restraints weight = 25618.813| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.43 r_work: 0.3654 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22384 Z= 0.174 Angle : 0.665 12.057 30498 Z= 0.327 Chirality : 0.045 0.308 3422 Planarity : 0.004 0.065 3790 Dihedral : 6.071 59.733 3565 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.72 % Favored : 93.05 % Rotamer: Outliers : 3.42 % Allowed : 21.17 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.00 (0.16), residues: 2648 helix: 0.28 (0.13), residues: 1620 sheet: -1.41 (0.56), residues: 70 loop : -2.22 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 149 HIS 0.014 0.001 HIS D 115 PHE 0.023 0.002 PHE D 110 TYR 0.018 0.001 TYR C 202 ARG 0.004 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00786 ( 18) link_NAG-ASN : angle 3.04827 ( 54) link_BETA1-4 : bond 0.00477 ( 14) link_BETA1-4 : angle 1.84849 ( 42) hydrogen bonds : bond 0.04847 ( 1037) hydrogen bonds : angle 4.28218 ( 3045) metal coordination : bond 0.00288 ( 4) SS BOND : bond 0.00754 ( 10) SS BOND : angle 2.13489 ( 20) covalent geometry : bond 0.00412 (22338) covalent geometry : angle 0.64767 (30382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 250 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8598 (t0) cc_final: 0.8303 (t0) REVERT: A 474 MET cc_start: 0.8709 (mmp) cc_final: 0.8439 (mmp) REVERT: A 479 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8264 (mt-10) REVERT: A 768 ARG cc_start: -0.1551 (OUTLIER) cc_final: -0.3953 (mpp80) REVERT: B 27 ASN cc_start: 0.6147 (OUTLIER) cc_final: 0.5297 (m110) REVERT: C 330 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8220 (p0) REVERT: C 495 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7867 (mm-30) REVERT: C 564 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: C 634 GLU cc_start: 0.8073 (pt0) cc_final: 0.7757 (pt0) REVERT: C 662 MET cc_start: 0.8632 (tpp) cc_final: 0.8328 (tpt) REVERT: C 667 GLU cc_start: 0.7441 (mp0) cc_final: 0.7098 (mp0) REVERT: C 750 MET cc_start: 0.3939 (ptt) cc_final: 0.3661 (ptp) REVERT: D 69 MET cc_start: 0.5147 (mmt) cc_final: 0.4925 (mmt) REVERT: D 139 CYS cc_start: 0.4800 (OUTLIER) cc_final: 0.4319 (t) REVERT: D 149 TRP cc_start: 0.6478 (t60) cc_final: 0.6196 (t60) REVERT: D 205 CYS cc_start: 0.5597 (OUTLIER) cc_final: 0.4948 (m) outliers start: 79 outliers final: 51 residues processed: 312 average time/residue: 0.2901 time to fit residues: 147.6114 Evaluate side-chains 281 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 136 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 233 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 252 optimal weight: 20.0000 chunk 146 optimal weight: 0.4980 chunk 257 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.232619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.189542 restraints weight = 25495.444| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.42 r_work: 0.3639 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22384 Z= 0.208 Angle : 0.673 11.795 30498 Z= 0.332 Chirality : 0.045 0.331 3422 Planarity : 0.004 0.051 3790 Dihedral : 5.882 58.254 3564 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.72 % Favored : 93.05 % Rotamer: Outliers : 3.25 % Allowed : 22.29 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.16), residues: 2648 helix: 0.35 (0.13), residues: 1624 sheet: -1.27 (0.56), residues: 70 loop : -2.22 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 149 HIS 0.009 0.001 HIS A 241 PHE 0.020 0.002 PHE A 314 TYR 0.022 0.002 TYR D 182 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00750 ( 18) link_NAG-ASN : angle 2.94488 ( 54) link_BETA1-4 : bond 0.00372 ( 14) link_BETA1-4 : angle 1.79624 ( 42) hydrogen bonds : bond 0.05003 ( 1037) hydrogen bonds : angle 4.26899 ( 3045) metal coordination : bond 0.00683 ( 4) SS BOND : bond 0.00847 ( 10) SS BOND : angle 2.29148 ( 20) covalent geometry : bond 0.00502 (22338) covalent geometry : angle 0.65635 (30382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 242 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8647 (t0) cc_final: 0.8312 (t0) REVERT: A 416 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8450 (tptp) REVERT: A 474 MET cc_start: 0.8801 (mmp) cc_final: 0.8557 (mmp) REVERT: A 479 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8179 (mt-10) REVERT: A 722 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9050 (tp) REVERT: A 768 ARG cc_start: -0.1404 (OUTLIER) cc_final: -0.3870 (mpp80) REVERT: B 101 TYR cc_start: 0.7453 (p90) cc_final: 0.7228 (p90) REVERT: C 269 ASP cc_start: 0.7822 (t0) cc_final: 0.7422 (t70) REVERT: C 376 MET cc_start: 0.8595 (ttm) cc_final: 0.8280 (ttt) REVERT: C 480 MET cc_start: 0.9110 (mtp) cc_final: 0.8868 (mtm) REVERT: C 495 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7930 (mm-30) REVERT: C 634 GLU cc_start: 0.8232 (pt0) cc_final: 0.7887 (pt0) REVERT: C 662 MET cc_start: 0.8537 (tpp) cc_final: 0.8196 (tmm) REVERT: C 667 GLU cc_start: 0.7499 (mp0) cc_final: 0.7188 (mp0) REVERT: C 668 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: D 69 MET cc_start: 0.5223 (mmt) cc_final: 0.4988 (mmt) REVERT: D 139 CYS cc_start: 0.4941 (OUTLIER) cc_final: 0.4579 (t) REVERT: D 205 CYS cc_start: 0.5582 (OUTLIER) cc_final: 0.4910 (m) outliers start: 75 outliers final: 52 residues processed: 301 average time/residue: 0.2863 time to fit residues: 142.3481 Evaluate side-chains 285 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.5402 > 50: distance: 38 - 45: 33.513 distance: 45 - 46: 39.036 distance: 46 - 47: 30.102 distance: 46 - 49: 31.555 distance: 47 - 48: 42.833 distance: 47 - 51: 37.857 distance: 49 - 50: 25.475 distance: 51 - 52: 50.079 distance: 52 - 53: 46.989 distance: 52 - 55: 40.208 distance: 53 - 54: 45.390 distance: 53 - 58: 53.070 distance: 55 - 56: 44.032 distance: 55 - 57: 47.301 distance: 58 - 59: 32.178 distance: 59 - 60: 16.518 distance: 59 - 62: 51.978 distance: 60 - 61: 61.049 distance: 60 - 64: 32.593 distance: 62 - 63: 23.317 distance: 63 - 138: 32.495 distance: 64 - 65: 57.766 distance: 64 - 70: 23.823 distance: 65 - 66: 35.209 distance: 65 - 68: 45.695 distance: 66 - 67: 28.871 distance: 66 - 71: 38.294 distance: 68 - 69: 40.896 distance: 69 - 70: 22.763 distance: 71 - 72: 19.847 distance: 72 - 73: 31.608 distance: 72 - 75: 20.021 distance: 73 - 74: 21.479 distance: 73 - 79: 30.468 distance: 75 - 76: 24.971 distance: 76 - 77: 34.295 distance: 76 - 78: 30.273 distance: 79 - 80: 38.833 distance: 80 - 81: 45.381 distance: 80 - 83: 33.543 distance: 81 - 82: 52.580 distance: 81 - 87: 41.400 distance: 83 - 84: 21.111 distance: 84 - 85: 16.950 distance: 84 - 86: 10.374 distance: 87 - 88: 54.411 distance: 88 - 89: 35.147 distance: 89 - 90: 56.302 distance: 89 - 91: 41.622 distance: 91 - 92: 39.676 distance: 92 - 93: 41.002 distance: 92 - 95: 31.473 distance: 93 - 94: 42.596 distance: 93 - 99: 37.783 distance: 95 - 96: 43.049 distance: 96 - 97: 19.904 distance: 96 - 98: 35.454 distance: 98 - 151: 12.973 distance: 99 - 100: 32.098 distance: 100 - 101: 56.403 distance: 100 - 103: 53.717 distance: 101 - 102: 42.802 distance: 101 - 109: 33.262 distance: 103 - 104: 8.144 distance: 104 - 105: 50.319 distance: 104 - 106: 22.140 distance: 105 - 107: 36.730 distance: 106 - 108: 35.220 distance: 107 - 108: 29.114 distance: 109 - 110: 43.160 distance: 110 - 111: 42.577 distance: 110 - 113: 39.409 distance: 111 - 112: 53.350 distance: 111 - 116: 29.488 distance: 113 - 114: 43.388 distance: 113 - 115: 47.889