Starting phenix.real_space_refine on Sat Jun 28 22:09:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pnm_13549/06_2025/7pnm_13549.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pnm_13549/06_2025/7pnm_13549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pnm_13549/06_2025/7pnm_13549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pnm_13549/06_2025/7pnm_13549.map" model { file = "/net/cci-nas-00/data/ceres_data/7pnm_13549/06_2025/7pnm_13549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pnm_13549/06_2025/7pnm_13549.cif" } resolution = 3.7 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 207 5.16 5 C 21303 2.51 5 N 5487 2.21 5 O 6543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33540 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "C" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "E" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} 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: "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: "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: "S" 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: "T" 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: "U" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 18.50, per 1000 atoms: 0.55 Number of scatterers: 33540 At special positions: 0 Unit cell: (191.7, 207.675, 161.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 207 16.00 O 6543 8.00 N 5487 7.00 C 21303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 197 " distance=2.04 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 390 " - pdb=" SG CYS A 606 " distance=2.05 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 583 " - pdb=" SG CYS A 589 " distance=2.04 Simple disulfide: pdb=" SG CYS A 622 " - pdb=" SG CYS A 675 " distance=2.04 Simple disulfide: pdb=" SG CYS A 700 " - pdb=" SG CYS A 725 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 840 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 930 " - pdb=" SG CYS A 941 " distance=2.03 Simple disulfide: pdb=" SG CYS A1118 " - pdb=" SG CYS A1129 " distance=2.04 Simple disulfide: pdb=" SG CYS A1168 " - pdb=" SG CYS A1213 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 197 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 606 " distance=2.05 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 514 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 583 " - pdb=" SG CYS B 589 " distance=2.04 Simple disulfide: pdb=" SG CYS B 622 " - pdb=" SG CYS B 675 " distance=2.04 Simple disulfide: pdb=" SG CYS B 700 " - pdb=" SG CYS B 725 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 818 " - pdb=" SG CYS B 840 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 829 " distance=2.03 Simple disulfide: pdb=" SG CYS B 930 " - pdb=" SG CYS B 941 " distance=2.03 Simple disulfide: pdb=" SG CYS B1118 " - pdb=" SG CYS B1129 " distance=2.04 Simple disulfide: pdb=" SG CYS B1168 " - pdb=" SG CYS B1213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 197 " distance=2.04 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 256 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 390 " - pdb=" SG CYS C 606 " distance=2.04 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 514 " distance=2.03 Simple disulfide: pdb=" SG CYS C 493 " - pdb=" SG CYS C 568 " distance=2.03 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 540 " distance=2.03 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 570 " distance=2.03 Simple disulfide: pdb=" SG CYS C 583 " - pdb=" SG CYS C 589 " distance=2.04 Simple disulfide: pdb=" SG CYS C 622 " - pdb=" SG CYS C 675 " distance=2.04 Simple disulfide: pdb=" SG CYS C 700 " - pdb=" SG CYS C 725 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 818 " - pdb=" SG CYS C 840 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 829 " distance=2.03 Simple disulfide: pdb=" SG CYS C 930 " - pdb=" SG CYS C 941 " distance=2.03 Simple disulfide: pdb=" SG CYS C1118 " - pdb=" SG CYS C1129 " distance=2.04 Simple disulfide: pdb=" SG CYS C1168 " - pdb=" SG CYS C1213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 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 F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1401 " - " ASN A 441 " " NAG A1402 " - " ASN A 640 " " NAG A1403 " - " ASN A 731 " " NAG A1404 " - " ASN A 59 " " NAG A1405 " - " ASN A 146 " " NAG A1406 " - " ASN A 667 " " NAG A1407 " - " ASN A 687 " " NAG A1408 " - " ASN A 706 " " NAG B1401 " - " ASN B 441 " " NAG B1402 " - " ASN B 640 " " NAG B1403 " - " ASN B 731 " " NAG B1404 " - " ASN B 59 " " NAG B1405 " - " ASN B 146 " " NAG B1406 " - " ASN B 667 " " NAG B1407 " - " ASN B 687 " " NAG B1408 " - " ASN B 706 " " NAG C1401 " - " ASN C 441 " " NAG C1402 " - " ASN C 640 " " NAG C1403 " - " ASN C 731 " " NAG C1404 " - " ASN C 59 " " NAG C1405 " - " ASN C 146 " " NAG C1406 " - " ASN C 667 " " NAG C1407 " - " ASN C 687 " " NAG C1408 " - " ASN C 706 " " NAG F 1 " - " ASN A 133 " " NAG J 1 " - " ASN A 202 " " NAG K 1 " - " ASN A 363 " " NAG M 1 " - " ASN A 929 " " NAG N 1 " - " ASN B 133 " " NAG O 1 " - " ASN B 202 " " NAG P 1 " - " ASN B 363 " " NAG Q 1 " - " ASN B 929 " " NAG R 1 " - " ASN C 133 " " NAG S 1 " - " ASN C 202 " " NAG T 1 " - " ASN C 363 " " NAG U 1 " - " ASN C 929 " Time building additional restraints: 7.86 Conformation dependent library (CDL) restraints added in 4.1 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7854 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 84 sheets defined 21.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.563A pdb=" N TRP A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.765A pdb=" N LEU A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.598A pdb=" N LEU A 409 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.507A pdb=" N LYS A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.718A pdb=" N VAL A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.627A pdb=" N PHE A 705 " --> pdb=" O CYS A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.990A pdb=" N VAL A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 866 removed outlier: 3.717A pdb=" N CYS A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.676A pdb=" N GLY A 878 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 915 removed outlier: 3.626A pdb=" N LYS A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 930 removed outlier: 4.095A pdb=" N CYS A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 946 removed outlier: 3.500A pdb=" N LYS A 946 " --> pdb=" O VAL A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 973 Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 1000 through 1004 removed outlier: 3.793A pdb=" N SER A1003 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1023 Processing helix chain 'A' and resid 1028 through 1050 Processing helix chain 'A' and resid 1051 through 1053 No H-bonds generated for 'chain 'A' and resid 1051 through 1053' Processing helix chain 'A' and resid 1062 through 1070 Processing helix chain 'A' and resid 1071 through 1118 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.875A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.700A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.909A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 removed outlier: 3.529A pdb=" N ASP H 104 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 336 through 342 removed outlier: 3.591A pdb=" N TRP B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.769A pdb=" N LEU B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.600A pdb=" N LEU B 409 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.506A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.747A pdb=" N VAL B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.605A pdb=" N PHE B 705 " --> pdb=" O CYS B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 826 through 834 removed outlier: 3.977A pdb=" N VAL B 834 " --> pdb=" O LYS B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 866 removed outlier: 3.737A pdb=" N CYS B 840 " --> pdb=" O TYR B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 878 removed outlier: 3.667A pdb=" N GLY B 878 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 915 removed outlier: 3.570A pdb=" N LYS B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 930 removed outlier: 4.116A pdb=" N CYS B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 946 removed outlier: 3.506A pdb=" N LYS B 946 " --> pdb=" O VAL B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 973 Processing helix chain 'B' and resid 983 through 994 Processing helix chain 'B' and resid 1000 through 1004 removed outlier: 3.834A pdb=" N SER B1003 " --> pdb=" O ASP B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1023 Processing helix chain 'B' and resid 1028 through 1050 Processing helix chain 'B' and resid 1051 through 1053 No H-bonds generated for 'chain 'B' and resid 1051 through 1053' Processing helix chain 'B' and resid 1062 through 1070 Processing helix chain 'B' and resid 1071 through 1118 Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.892A pdb=" N VAL D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.718A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.877A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 105 removed outlier: 3.532A pdb=" N ASP G 104 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 293 through 302 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.587A pdb=" N TRP C 340 " --> pdb=" O ASN C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.768A pdb=" N LEU C 367 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.586A pdb=" N LEU C 409 " --> pdb=" O LYS C 406 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 450 through 456 removed outlier: 3.548A pdb=" N LYS C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 464 removed outlier: 3.733A pdb=" N VAL C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 700 through 708 removed outlier: 3.613A pdb=" N PHE C 705 " --> pdb=" O CYS C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 823 Processing helix chain 'C' and resid 826 through 834 removed outlier: 3.988A pdb=" N VAL C 834 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 866 removed outlier: 3.740A pdb=" N CYS C 840 " --> pdb=" O TYR C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 878 removed outlier: 3.669A pdb=" N GLY C 878 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 915 removed outlier: 3.561A pdb=" N LYS C 915 " --> pdb=" O LEU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 930 removed outlier: 4.071A pdb=" N CYS C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 946 removed outlier: 3.510A pdb=" N LYS C 946 " --> pdb=" O VAL C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 973 Processing helix chain 'C' and resid 983 through 994 Processing helix chain 'C' and resid 1000 through 1004 removed outlier: 3.799A pdb=" N SER C1003 " --> pdb=" O ASP C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1023 Processing helix chain 'C' and resid 1028 through 1050 Processing helix chain 'C' and resid 1051 through 1053 No H-bonds generated for 'chain 'C' and resid 1051 through 1053' Processing helix chain 'C' and resid 1062 through 1070 Processing helix chain 'C' and resid 1071 through 1118 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.882A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.720A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.867A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 105 removed outlier: 3.525A pdb=" N ASP I 104 " --> pdb=" O GLN I 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 69 removed outlier: 4.604A pdb=" N GLU A 263 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 108 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 213 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 217 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE A 223 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN A 239 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA A 225 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 237 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 69 removed outlier: 3.845A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.195A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.761A pdb=" N VAL A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 141 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 161 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 199 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.761A pdb=" N VAL A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 141 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 205 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 313 removed outlier: 3.901A pdb=" N PHE A 684 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AB1, first strand: chain 'A' and resid 323 through 327 removed outlier: 3.677A pdb=" N GLY A 632 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR A 659 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 660 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 358 removed outlier: 3.784A pdb=" N GLU A 353 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 398 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 355 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 396 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 375 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN A 436 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ALA A 373 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 353 through 358 removed outlier: 3.784A pdb=" N GLU A 353 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 398 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 355 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 396 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AB5, first strand: chain 'A' and resid 476 through 480 Processing sheet with id=AB6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.327A pdb=" N CYS A 483 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 543 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AB8, first strand: chain 'A' and resid 730 through 737 removed outlier: 7.373A pdb=" N TYR A 730 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N ASN A 770 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N SER A 732 " --> pdb=" O ASN A 770 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 742 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 777 through 779 removed outlier: 5.819A pdb=" N ASN A 777 " --> pdb=" O LEU B 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 790 through 800 removed outlier: 3.698A pdb=" N ILE A 792 " --> pdb=" O ALA A1161 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A1161 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS A1157 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 798 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A 800 " --> pdb=" O TYR A1153 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR A1153 " --> pdb=" O ILE A 800 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 790 through 800 removed outlier: 3.698A pdb=" N ILE A 792 " --> pdb=" O ALA A1161 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A1161 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS A1157 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 798 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A 800 " --> pdb=" O TYR A1153 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR A1153 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A1145 " --> pdb=" O ALA A1142 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A1142 " --> pdb=" O GLY A1145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A1136 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR A1153 " --> pdb=" O HIS A1134 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS A1134 " --> pdb=" O TYR A1153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 814 through 816 Processing sheet with id=AC4, first strand: chain 'A' and resid 870 through 872 Processing sheet with id=AC5, first strand: chain 'A' and resid 882 through 883 removed outlier: 3.544A pdb=" N VAL A 883 " --> pdb=" O ILE A 886 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1207 through 1210 removed outlier: 3.698A pdb=" N ALA A1176 " --> pdb=" O VAL A1208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1167 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1181 through 1185 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.625A pdb=" N VAL L 13 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL L 90 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN L 43 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET L 94 " --> pdb=" O ASP L 39 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP L 39 " --> pdb=" O MET L 94 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.268A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.253A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AD4, first strand: chain 'B' and resid 61 through 69 removed outlier: 4.585A pdb=" N GLU B 263 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 108 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 213 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 217 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 222 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 238 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE B 227 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE B 236 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 61 through 69 removed outlier: 3.783A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 81 through 82 removed outlier: 8.372A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TRP B 188 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.764A pdb=" N VAL B 139 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 141 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 161 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 199 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.764A pdb=" N VAL B 139 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 141 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 205 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AE1, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.862A pdb=" N PHE B 684 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 681 " --> pdb=" O LEU B 694 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 323 through 327 removed outlier: 3.732A pdb=" N GLY B 632 " --> pdb=" O TYR B 625 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR B 659 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 660 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.837A pdb=" N LYS B 355 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 396 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 430 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 375 " --> pdb=" O TYR B 434 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN B 436 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA B 373 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.837A pdb=" N LYS B 355 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 396 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 Processing sheet with id=AE6, first strand: chain 'B' and resid 476 through 480 Processing sheet with id=AE7, first strand: chain 'B' and resid 483 through 485 removed outlier: 4.272A pdb=" N CYS B 483 " --> pdb=" O SER B 545 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 543 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AE9, first strand: chain 'B' and resid 730 through 737 removed outlier: 7.322A pdb=" N TYR B 730 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ASN B 770 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N SER B 732 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B 748 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 742 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 777 through 779 removed outlier: 5.825A pdb=" N ASN B 777 " --> pdb=" O LEU C 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 790 through 800 removed outlier: 3.718A pdb=" N ILE B 792 " --> pdb=" O ALA B1161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B1161 " --> pdb=" O ILE B 792 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS B1157 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 798 " --> pdb=" O PRO B1155 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE B 800 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR B1153 " --> pdb=" O ILE B 800 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 790 through 800 removed outlier: 3.718A pdb=" N ILE B 792 " --> pdb=" O ALA B1161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B1161 " --> pdb=" O ILE B 792 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS B1157 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 798 " --> pdb=" O PRO B1155 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE B 800 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR B1153 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B1145 " --> pdb=" O ALA B1142 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B1142 " --> pdb=" O GLY B1145 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE B1136 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR B1153 " --> pdb=" O HIS B1134 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS B1134 " --> pdb=" O TYR B1153 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 814 through 816 Processing sheet with id=AF5, first strand: chain 'B' and resid 882 through 883 removed outlier: 3.550A pdb=" N VAL B 883 " --> pdb=" O ILE B 886 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1207 through 1210 removed outlier: 3.679A pdb=" N ALA B1176 " --> pdb=" O VAL B1208 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B1167 " --> pdb=" O ILE B1175 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 1181 through 1185 Processing sheet with id=AF8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.641A pdb=" N VAL D 13 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D 90 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN D 43 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET D 94 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP D 39 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AG1, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.287A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU G 20 " --> pdb=" O LEU G 81 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.516A pdb=" N THR G 118 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 117 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 50 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR G 59 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AG4, first strand: chain 'C' and resid 61 through 69 removed outlier: 4.642A pdb=" N GLU C 263 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 108 " --> pdb=" O GLU C 263 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 213 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 217 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 61 through 69 removed outlier: 3.753A pdb=" N ASN C 286 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 81 through 82 removed outlier: 8.374A pdb=" N THR C 255 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TRP C 188 " --> pdb=" O CYS C 169 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.755A pdb=" N VAL C 139 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 141 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 161 " --> pdb=" O ARG C 201 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 199 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.755A pdb=" N VAL C 139 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 141 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR C 205 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AH1, first strand: chain 'C' and resid 310 through 313 removed outlier: 3.883A pdb=" N PHE C 684 " --> pdb=" O GLY C 310 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 317 through 318 removed outlier: 3.550A pdb=" N TYR C 317 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 678 " --> pdb=" O TYR C 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'C' and resid 323 through 327 removed outlier: 3.720A pdb=" N GLY C 632 " --> pdb=" O TYR C 625 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR C 659 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY C 660 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.776A pdb=" N GLU C 353 " --> pdb=" O LYS C 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 398 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 430 " --> pdb=" O ASN C 379 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 375 " --> pdb=" O TYR C 434 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN C 436 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA C 373 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.170A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 361 through 362 Processing sheet with id=AH7, first strand: chain 'C' and resid 476 through 480 Processing sheet with id=AH8, first strand: chain 'C' and resid 483 through 485 removed outlier: 4.325A pdb=" N CYS C 483 " --> pdb=" O SER C 545 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 543 " --> pdb=" O LYS C 485 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 557 through 558 Processing sheet with id=AI1, first strand: chain 'C' and resid 730 through 737 removed outlier: 7.307A pdb=" N TYR C 730 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASN C 770 " --> pdb=" O TYR C 730 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N SER C 732 " --> pdb=" O ASN C 770 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR C 748 " --> pdb=" O VAL C 744 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 742 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 790 through 800 removed outlier: 3.728A pdb=" N ILE C 792 " --> pdb=" O ALA C1161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C1161 " --> pdb=" O ILE C 792 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS C1157 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 798 " --> pdb=" O PRO C1155 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE C 800 " --> pdb=" O TYR C1153 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C1153 " --> pdb=" O ILE C 800 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 790 through 800 removed outlier: 3.728A pdb=" N ILE C 792 " --> pdb=" O ALA C1161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C1161 " --> pdb=" O ILE C 792 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS C1157 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 798 " --> pdb=" O PRO C1155 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE C 800 " --> pdb=" O TYR C1153 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C1153 " --> pdb=" O ILE C 800 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C1145 " --> pdb=" O ALA C1142 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C1142 " --> pdb=" O GLY C1145 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE C1136 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C1153 " --> pdb=" O HIS C1134 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS C1134 " --> pdb=" O TYR C1153 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 814 through 816 Processing sheet with id=AI5, first strand: chain 'C' and resid 882 through 883 removed outlier: 3.544A pdb=" N VAL C 883 " --> pdb=" O ILE C 886 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 1167 through 1168 Processing sheet with id=AI7, first strand: chain 'C' and resid 1174 through 1177 removed outlier: 3.647A pdb=" N ALA C1176 " --> pdb=" O VAL C1208 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 1181 through 1185 Processing sheet with id=AI9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.652A pdb=" N VAL E 13 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 90 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 43 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET E 94 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP E 39 " --> pdb=" O MET E 94 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AJ2, first strand: chain 'I' and resid 3 through 7 removed outlier: 4.279A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU I 20 " --> pdb=" O LEU I 81 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.534A pdb=" N THR I 118 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL I 50 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR I 59 " --> pdb=" O VAL I 50 " (cutoff:3.500A) 1246 hydrogen bonds defined for protein. 3411 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: 19.78 Time building geometry restraints manager: 9.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10653 1.34 - 1.47: 8740 1.47 - 1.59: 14630 1.59 - 1.72: 0 1.72 - 1.84: 273 Bond restraints: 34296 Sorted by residual: bond pdb=" C1 NAG C1404 " pdb=" O5 NAG C1404 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C1 NAG A1404 " pdb=" O5 NAG A1404 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C1 NAG B1404 " pdb=" O5 NAG B1404 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" C1 NAG C1405 " pdb=" O5 NAG C1405 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.62e+00 ... (remaining 34291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 45864 2.50 - 5.01: 708 5.01 - 7.51: 76 7.51 - 10.02: 26 10.02 - 12.52: 3 Bond angle restraints: 46677 Sorted by residual: angle pdb=" N GLN B 860 " pdb=" CA GLN B 860 " pdb=" CB GLN B 860 " ideal model delta sigma weight residual 110.16 116.23 -6.07 1.48e+00 4.57e-01 1.68e+01 angle pdb=" N GLN A 860 " pdb=" CA GLN A 860 " pdb=" CB GLN A 860 " ideal model delta sigma weight residual 110.16 116.17 -6.01 1.48e+00 4.57e-01 1.65e+01 angle pdb=" C ASN B1186 " pdb=" N ASN B1187 " pdb=" CA ASN B1187 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" N VAL G 64 " pdb=" CA VAL G 64 " pdb=" C VAL G 64 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" C ASN C1186 " pdb=" N ASN C1187 " pdb=" CA ASN C1187 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 ... (remaining 46672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.53: 19813 23.53 - 47.05: 1049 47.05 - 70.58: 102 70.58 - 94.11: 33 94.11 - 117.63: 9 Dihedral angle restraints: 21006 sinusoidal: 8703 harmonic: 12303 Sorted by residual: dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 197 " pdb=" CB CYS A 197 " ideal model delta sinusoidal sigma weight residual 93.00 33.11 59.89 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS B 164 " pdb=" SG CYS B 164 " pdb=" SG CYS B 197 " pdb=" CB CYS B 197 " ideal model delta sinusoidal sigma weight residual 93.00 33.14 59.86 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS C 164 " pdb=" SG CYS C 164 " pdb=" SG CYS C 197 " pdb=" CB CYS C 197 " ideal model delta sinusoidal sigma weight residual 93.00 33.75 59.25 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 21003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4574 0.074 - 0.149: 738 0.149 - 0.223: 58 0.223 - 0.297: 3 0.297 - 0.371: 3 Chirality restraints: 5376 Sorted by residual: chirality pdb=" C1 NAG B1405 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B1405 " pdb=" O5 NAG B1405 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C1 NAG C1405 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C1405 " pdb=" O5 NAG C1405 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C1 NAG A1405 " pdb=" ND2 ASN A 146 " pdb=" C2 NAG A1405 " pdb=" O5 NAG A1405 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 5373 not shown) Planarity restraints: 5988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 772 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO C 773 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 773 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 773 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 92 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 93 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 92 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 93 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.026 5.00e-02 4.00e+02 ... (remaining 5985 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 8672 2.80 - 3.32: 27854 3.32 - 3.85: 55776 3.85 - 4.37: 62158 4.37 - 4.90: 109433 Nonbonded interactions: 263893 Sorted by model distance: nonbonded pdb=" O GLU C 852 " pdb=" OG1 THR C 856 " model vdw 2.275 3.040 nonbonded pdb=" O GLU B 852 " pdb=" OG1 THR B 856 " model vdw 2.278 3.040 nonbonded pdb=" O GLU A 852 " pdb=" OG1 THR A 856 " model vdw 2.287 3.040 nonbonded pdb=" OD2 ASP A 397 " pdb=" OH TYR A 422 " model vdw 2.291 3.040 nonbonded pdb=" OD2 ASP B 397 " pdb=" OH TYR B 422 " model vdw 2.296 3.040 ... (remaining 263888 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 0.040 Extract box with map and model: 1.400 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 81.950 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 : 0.004 0.095 34413 Z= 0.197 Angle : 0.768 12.896 46959 Z= 0.397 Chirality : 0.053 0.371 5376 Planarity : 0.005 0.048 5952 Dihedral : 13.599 117.634 12945 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.11 (0.12), residues: 4176 helix: -1.65 (0.16), residues: 750 sheet: -0.88 (0.16), residues: 981 loop : -1.54 (0.11), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 40 HIS 0.006 0.001 HIS H 35 PHE 0.018 0.001 PHE A 122 TYR 0.028 0.002 TYR B 317 ARG 0.003 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 36) link_NAG-ASN : angle 2.77708 ( 108) link_BETA1-4 : bond 0.00555 ( 12) link_BETA1-4 : angle 1.47402 ( 36) hydrogen bonds : bond 0.22987 ( 1134) hydrogen bonds : angle 9.55135 ( 3411) SS BOND : bond 0.00465 ( 69) SS BOND : angle 1.62332 ( 138) covalent geometry : bond 0.00393 (34296) covalent geometry : angle 0.75232 (46677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 944 time to evaluate : 3.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7116 (mmm) cc_final: 0.6843 (tpt) REVERT: A 180 LEU cc_start: 0.8557 (mt) cc_final: 0.8246 (mt) REVERT: A 259 LYS cc_start: 0.7852 (ptmt) cc_final: 0.7435 (ptmt) REVERT: A 315 ASN cc_start: 0.7542 (p0) cc_final: 0.7304 (p0) REVERT: A 329 LYS cc_start: 0.7537 (mmmm) cc_final: 0.7328 (ttmm) REVERT: A 425 ASP cc_start: 0.7202 (t70) cc_final: 0.6924 (t0) REVERT: A 437 LEU cc_start: 0.8001 (mt) cc_final: 0.7513 (mt) REVERT: A 626 ASP cc_start: 0.6826 (t0) cc_final: 0.6348 (t0) REVERT: A 1000 ASP cc_start: 0.7427 (t0) cc_final: 0.6994 (t0) REVERT: A 1005 ASN cc_start: 0.7344 (t0) cc_final: 0.7022 (t0) REVERT: A 1035 GLN cc_start: 0.7499 (tp40) cc_final: 0.7243 (tp40) REVERT: A 1060 SER cc_start: 0.7642 (t) cc_final: 0.7421 (t) REVERT: A 1079 ILE cc_start: 0.7571 (mt) cc_final: 0.7043 (mt) REVERT: A 1087 LEU cc_start: 0.7615 (mt) cc_final: 0.7192 (mt) REVERT: A 1182 PHE cc_start: 0.7508 (m-80) cc_final: 0.7206 (m-80) REVERT: A 1187 ASN cc_start: 0.8835 (p0) cc_final: 0.8630 (p0) REVERT: L 75 ASP cc_start: 0.7330 (p0) cc_final: 0.6712 (m-30) REVERT: H 103 LEU cc_start: 0.8925 (tp) cc_final: 0.8207 (tt) REVERT: B 29 LYS cc_start: 0.7540 (tptt) cc_final: 0.7118 (ttpp) REVERT: B 78 MET cc_start: 0.7007 (mmm) cc_final: 0.6699 (tpt) REVERT: B 106 LYS cc_start: 0.6938 (tptp) cc_final: 0.6607 (ttmm) REVERT: B 180 LEU cc_start: 0.8530 (mt) cc_final: 0.8238 (mt) REVERT: B 235 LYS cc_start: 0.7624 (mtmm) cc_final: 0.7412 (mtmm) REVERT: B 259 LYS cc_start: 0.7648 (ptmt) cc_final: 0.7300 (ptmt) REVERT: B 423 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7424 (mmm-85) REVERT: B 437 LEU cc_start: 0.7816 (mt) cc_final: 0.7500 (mt) REVERT: B 478 VAL cc_start: 0.8206 (p) cc_final: 0.7853 (m) REVERT: B 596 ILE cc_start: 0.8737 (mm) cc_final: 0.8205 (mm) REVERT: B 597 LEU cc_start: 0.8472 (mt) cc_final: 0.8239 (mt) REVERT: B 626 ASP cc_start: 0.7021 (t0) cc_final: 0.6473 (t0) REVERT: B 662 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.7041 (mtp-110) REVERT: B 668 ARG cc_start: 0.7499 (mtp85) cc_final: 0.7287 (mtm-85) REVERT: B 697 ASN cc_start: 0.7013 (m-40) cc_final: 0.6695 (m-40) REVERT: B 720 ASP cc_start: 0.7295 (m-30) cc_final: 0.6661 (m-30) REVERT: B 808 GLN cc_start: 0.6900 (pt0) cc_final: 0.6582 (pt0) REVERT: B 923 PHE cc_start: 0.7519 (m-80) cc_final: 0.6991 (m-80) REVERT: B 958 ASN cc_start: 0.7404 (m110) cc_final: 0.7023 (m-40) REVERT: B 963 TYR cc_start: 0.7486 (m-10) cc_final: 0.7161 (m-80) REVERT: B 1035 GLN cc_start: 0.7703 (tp40) cc_final: 0.7499 (tp40) REVERT: B 1039 ASN cc_start: 0.7666 (t0) cc_final: 0.7399 (t0) REVERT: B 1079 ILE cc_start: 0.7544 (mt) cc_final: 0.7288 (mt) REVERT: B 1087 LEU cc_start: 0.7457 (mt) cc_final: 0.6937 (mt) REVERT: B 1126 ILE cc_start: 0.8188 (mm) cc_final: 0.7944 (mm) REVERT: B 1139 VAL cc_start: 0.8449 (t) cc_final: 0.8016 (p) REVERT: B 1141 ASN cc_start: 0.8094 (t0) cc_final: 0.7792 (t0) REVERT: B 1182 PHE cc_start: 0.7531 (m-80) cc_final: 0.7144 (m-80) REVERT: B 1198 TYR cc_start: 0.7070 (t80) cc_final: 0.6860 (t80) REVERT: D 75 ASP cc_start: 0.7267 (p0) cc_final: 0.6877 (m-30) REVERT: G 103 LEU cc_start: 0.8938 (tp) cc_final: 0.8422 (tt) REVERT: G 105 TYR cc_start: 0.5107 (t80) cc_final: 0.4853 (t80) REVERT: C 29 LYS cc_start: 0.7446 (tptt) cc_final: 0.7082 (ttpp) REVERT: C 78 MET cc_start: 0.6854 (mmm) cc_final: 0.6517 (tpp) REVERT: C 180 LEU cc_start: 0.8471 (mt) cc_final: 0.8174 (mp) REVERT: C 237 LEU cc_start: 0.7747 (tp) cc_final: 0.7506 (tp) REVERT: C 259 LYS cc_start: 0.7625 (ptmt) cc_final: 0.7310 (ptmt) REVERT: C 344 LYS cc_start: 0.7878 (ttpp) cc_final: 0.7630 (ttmm) REVERT: C 382 ASP cc_start: 0.7507 (p0) cc_final: 0.7220 (p0) REVERT: C 422 TYR cc_start: 0.7138 (t80) cc_final: 0.6774 (t80) REVERT: C 425 ASP cc_start: 0.7126 (t70) cc_final: 0.6898 (t0) REVERT: C 461 ASP cc_start: 0.7154 (p0) cc_final: 0.6921 (p0) REVERT: C 478 VAL cc_start: 0.8435 (p) cc_final: 0.8112 (m) REVERT: C 596 ILE cc_start: 0.8820 (mm) cc_final: 0.8536 (mm) REVERT: C 689 SER cc_start: 0.7227 (t) cc_final: 0.7003 (t) REVERT: C 799 THR cc_start: 0.7556 (t) cc_final: 0.7346 (t) REVERT: C 855 ASP cc_start: 0.6530 (p0) cc_final: 0.6224 (p0) REVERT: C 1000 ASP cc_start: 0.7408 (t0) cc_final: 0.7177 (t0) REVERT: C 1039 ASN cc_start: 0.7579 (t0) cc_final: 0.7195 (t0) REVERT: C 1073 LEU cc_start: 0.6491 (pt) cc_final: 0.6170 (pt) REVERT: C 1079 ILE cc_start: 0.7612 (mt) cc_final: 0.7407 (mt) REVERT: C 1106 PHE cc_start: 0.6753 (t80) cc_final: 0.6409 (t80) REVERT: C 1154 VAL cc_start: 0.7880 (t) cc_final: 0.7670 (p) REVERT: C 1182 PHE cc_start: 0.7427 (m-80) cc_final: 0.7165 (m-80) REVERT: E 21 ILE cc_start: 0.8619 (mt) cc_final: 0.8414 (tp) REVERT: I 103 LEU cc_start: 0.8745 (tp) cc_final: 0.8449 (tt) outliers start: 5 outliers final: 0 residues processed: 949 average time/residue: 0.4386 time to fit residues: 680.7875 Evaluate side-chains 830 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 830 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 4.9990 chunk 318 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 170 optimal weight: 0.0270 chunk 329 optimal weight: 9.9990 chunk 127 optimal weight: 0.5980 chunk 200 optimal weight: 0.9980 chunk 245 optimal weight: 3.9990 chunk 381 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 410 GLN A 697 ASN A1064 GLN A1110 GLN L 31 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN B 410 GLN B 697 ASN B 777 ASN B 844 ASN B 928 ASN B1096 GLN B1134 HIS B1150 HIS G 13 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN C 844 ASN ** C 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 GLN C1096 GLN E 27 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.149019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.122719 restraints weight = 55933.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127430 restraints weight = 29026.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.130661 restraints weight = 17884.222| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34413 Z= 0.136 Angle : 0.629 8.963 46959 Z= 0.327 Chirality : 0.047 0.358 5376 Planarity : 0.004 0.040 5952 Dihedral : 7.663 104.116 5592 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.39 % Allowed : 9.43 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.12), residues: 4176 helix: -0.63 (0.17), residues: 765 sheet: -0.56 (0.17), residues: 951 loop : -1.25 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 102 HIS 0.005 0.001 HIS A 215 PHE 0.025 0.002 PHE C 203 TYR 0.026 0.002 TYR B1093 ARG 0.007 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 36) link_NAG-ASN : angle 2.05702 ( 108) link_BETA1-4 : bond 0.00365 ( 12) link_BETA1-4 : angle 1.17952 ( 36) hydrogen bonds : bond 0.04711 ( 1134) hydrogen bonds : angle 6.71209 ( 3411) SS BOND : bond 0.00485 ( 69) SS BOND : angle 1.12614 ( 138) covalent geometry : bond 0.00297 (34296) covalent geometry : angle 0.61968 (46677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 874 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8094 (tptt) cc_final: 0.7574 (tppt) REVERT: A 180 LEU cc_start: 0.8527 (mt) cc_final: 0.8254 (mt) REVERT: A 201 ARG cc_start: 0.7381 (ptm-80) cc_final: 0.7031 (ptm-80) REVERT: A 259 LYS cc_start: 0.7909 (ptmt) cc_final: 0.7412 (ptmt) REVERT: A 315 ASN cc_start: 0.7891 (p0) cc_final: 0.7445 (p0) REVERT: A 328 ARG cc_start: 0.7022 (mpt180) cc_final: 0.6503 (mpt180) REVERT: A 343 ASP cc_start: 0.7327 (t0) cc_final: 0.7046 (t0) REVERT: A 345 SER cc_start: 0.7596 (p) cc_final: 0.7203 (m) REVERT: A 375 SER cc_start: 0.7890 (t) cc_final: 0.7252 (m) REVERT: A 425 ASP cc_start: 0.7619 (t70) cc_final: 0.7137 (t0) REVERT: A 435 TYR cc_start: 0.7424 (p90) cc_final: 0.7101 (p90) REVERT: A 478 VAL cc_start: 0.8118 (p) cc_final: 0.7801 (m) REVERT: A 610 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.7860 (pp) REVERT: A 626 ASP cc_start: 0.7018 (t0) cc_final: 0.6353 (t0) REVERT: A 663 ASP cc_start: 0.7371 (t70) cc_final: 0.6785 (t0) REVERT: A 832 GLN cc_start: 0.7829 (mm110) cc_final: 0.7464 (mm110) REVERT: A 850 VAL cc_start: 0.8559 (m) cc_final: 0.8340 (p) REVERT: A 858 GLN cc_start: 0.7663 (mm110) cc_final: 0.7337 (mm-40) REVERT: A 860 GLN cc_start: 0.7283 (mp10) cc_final: 0.7071 (mp10) REVERT: A 923 PHE cc_start: 0.7860 (m-80) cc_final: 0.7626 (m-80) REVERT: A 958 ASN cc_start: 0.8238 (m-40) cc_final: 0.7993 (m-40) REVERT: A 1000 ASP cc_start: 0.7391 (t0) cc_final: 0.7057 (t0) REVERT: A 1035 GLN cc_start: 0.8248 (tp40) cc_final: 0.8019 (tp40) REVERT: A 1060 SER cc_start: 0.8258 (t) cc_final: 0.7802 (t) REVERT: A 1065 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6027 (mt-10) REVERT: A 1069 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7959 (mtm-85) REVERT: A 1076 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: A 1080 ASP cc_start: 0.7375 (t0) cc_final: 0.6982 (t0) REVERT: A 1113 GLU cc_start: 0.7694 (tt0) cc_final: 0.7478 (tt0) REVERT: A 1141 ASN cc_start: 0.8332 (t0) cc_final: 0.7754 (t0) REVERT: A 1177 PRO cc_start: 0.8011 (Cg_endo) cc_final: 0.7683 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7371 (m-80) cc_final: 0.6487 (m-80) REVERT: A 1190 MET cc_start: 0.7101 (ttt) cc_final: 0.6408 (ttt) REVERT: A 1191 TYR cc_start: 0.7394 (t80) cc_final: 0.7072 (t80) REVERT: L 31 HIS cc_start: 0.7305 (t70) cc_final: 0.6972 (t-170) REVERT: L 75 ASP cc_start: 0.7582 (p0) cc_final: 0.6757 (m-30) REVERT: H 52 TRP cc_start: 0.6915 (OUTLIER) cc_final: 0.6271 (t-100) REVERT: H 103 LEU cc_start: 0.8980 (tp) cc_final: 0.8288 (tt) REVERT: B 30 ASP cc_start: 0.7706 (t0) cc_final: 0.7477 (t0) REVERT: B 78 MET cc_start: 0.7636 (mmm) cc_final: 0.7379 (tpt) REVERT: B 180 LEU cc_start: 0.8597 (mt) cc_final: 0.8340 (mt) REVERT: B 201 ARG cc_start: 0.7374 (ptm-80) cc_final: 0.7010 (ptm-80) REVERT: B 259 LYS cc_start: 0.7815 (ptmt) cc_final: 0.7393 (ptmt) REVERT: B 312 TYR cc_start: 0.7790 (m-10) cc_final: 0.7544 (m-10) REVERT: B 313 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6918 (mm-30) REVERT: B 344 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7697 (ttmm) REVERT: B 418 GLN cc_start: 0.7904 (tt0) cc_final: 0.7642 (tt0) REVERT: B 423 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7661 (mmm-85) REVERT: B 435 TYR cc_start: 0.7451 (p90) cc_final: 0.7229 (p90) REVERT: B 478 VAL cc_start: 0.8185 (p) cc_final: 0.7915 (m) REVERT: B 596 ILE cc_start: 0.8468 (mm) cc_final: 0.8263 (mm) REVERT: B 662 ARG cc_start: 0.7810 (mtp-110) cc_final: 0.7535 (mtp-110) REVERT: B 689 SER cc_start: 0.7655 (t) cc_final: 0.7393 (t) REVERT: B 697 ASN cc_start: 0.7770 (m110) cc_final: 0.7403 (m-40) REVERT: B 772 GLU cc_start: 0.7446 (tp30) cc_final: 0.7001 (tp30) REVERT: B 852 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7685 (mt-10) REVERT: B 860 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: B 866 MET cc_start: 0.6186 (mmm) cc_final: 0.5962 (mtm) REVERT: B 923 PHE cc_start: 0.7806 (m-80) cc_final: 0.7486 (m-80) REVERT: B 958 ASN cc_start: 0.8189 (m110) cc_final: 0.7668 (m-40) REVERT: B 963 TYR cc_start: 0.8423 (m-10) cc_final: 0.7764 (m-80) REVERT: B 1051 GLN cc_start: 0.7443 (mp10) cc_final: 0.7175 (mp10) REVERT: B 1079 ILE cc_start: 0.8615 (mt) cc_final: 0.8330 (mt) REVERT: B 1087 LEU cc_start: 0.8558 (mt) cc_final: 0.8059 (mt) REVERT: B 1091 ASN cc_start: 0.8028 (m110) cc_final: 0.7826 (m110) REVERT: B 1139 VAL cc_start: 0.8614 (t) cc_final: 0.8206 (p) REVERT: B 1141 ASN cc_start: 0.8560 (t0) cc_final: 0.7936 (t0) REVERT: B 1182 PHE cc_start: 0.7346 (m-80) cc_final: 0.6821 (m-80) REVERT: B 1183 VAL cc_start: 0.7996 (t) cc_final: 0.7527 (m) REVERT: B 1189 TRP cc_start: 0.8388 (m100) cc_final: 0.8062 (m100) REVERT: B 1190 MET cc_start: 0.7041 (ttm) cc_final: 0.6469 (ttt) REVERT: D 75 ASP cc_start: 0.7557 (p0) cc_final: 0.7021 (m-30) REVERT: G 52 TRP cc_start: 0.6693 (OUTLIER) cc_final: 0.6030 (t-100) REVERT: G 102 TRP cc_start: 0.7595 (p-90) cc_final: 0.7310 (p-90) REVERT: G 103 LEU cc_start: 0.9119 (tp) cc_final: 0.8428 (tt) REVERT: C 180 LEU cc_start: 0.8590 (mt) cc_final: 0.8239 (mp) REVERT: C 235 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7627 (mtmm) REVERT: C 237 LEU cc_start: 0.8482 (tp) cc_final: 0.8110 (tp) REVERT: C 259 LYS cc_start: 0.7741 (ptmt) cc_final: 0.7445 (ptmt) REVERT: C 264 TYR cc_start: 0.6287 (t80) cc_final: 0.6049 (t80) REVERT: C 314 LEU cc_start: 0.8706 (mm) cc_final: 0.8469 (mp) REVERT: C 325 VAL cc_start: 0.7320 (p) cc_final: 0.7044 (m) REVERT: C 342 ASN cc_start: 0.8265 (t0) cc_final: 0.7827 (t0) REVERT: C 344 LYS cc_start: 0.7811 (ttpp) cc_final: 0.7497 (ttmm) REVERT: C 375 SER cc_start: 0.7630 (t) cc_final: 0.7249 (m) REVERT: C 376 PHE cc_start: 0.8231 (t80) cc_final: 0.8006 (t80) REVERT: C 422 TYR cc_start: 0.7229 (t80) cc_final: 0.6956 (t80) REVERT: C 425 ASP cc_start: 0.7599 (t70) cc_final: 0.7162 (t0) REVERT: C 435 TYR cc_start: 0.7505 (p90) cc_final: 0.7232 (p90) REVERT: C 460 GLU cc_start: 0.8190 (mp0) cc_final: 0.7925 (mp0) REVERT: C 478 VAL cc_start: 0.8263 (p) cc_final: 0.7987 (m) REVERT: C 494 LYS cc_start: 0.7641 (mmmt) cc_final: 0.7337 (mmmt) REVERT: C 626 ASP cc_start: 0.6998 (t0) cc_final: 0.5999 (t70) REVERT: C 662 ARG cc_start: 0.7701 (mtp-110) cc_final: 0.7405 (mtp-110) REVERT: C 689 SER cc_start: 0.7447 (t) cc_final: 0.7178 (t) REVERT: C 699 LYS cc_start: 0.8194 (mmmm) cc_final: 0.7502 (mtmm) REVERT: C 730 TYR cc_start: 0.6872 (p90) cc_final: 0.6451 (p90) REVERT: C 855 ASP cc_start: 0.7449 (p0) cc_final: 0.7221 (p0) REVERT: C 860 GLN cc_start: 0.7491 (mp10) cc_final: 0.6996 (mp10) REVERT: C 999 MET cc_start: 0.6629 (ttp) cc_final: 0.6067 (mtp) REVERT: C 1000 ASP cc_start: 0.7427 (t0) cc_final: 0.7048 (t0) REVERT: C 1005 ASN cc_start: 0.7524 (t0) cc_final: 0.7038 (t0) REVERT: C 1039 ASN cc_start: 0.8276 (t0) cc_final: 0.7832 (t0) REVERT: C 1041 ASN cc_start: 0.7627 (m110) cc_final: 0.7317 (p0) REVERT: C 1073 LEU cc_start: 0.7730 (pt) cc_final: 0.7252 (pt) REVERT: C 1074 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7088 (mm-30) REVERT: C 1083 ILE cc_start: 0.8683 (mt) cc_final: 0.8478 (mm) REVERT: C 1112 MET cc_start: 0.7632 (mmm) cc_final: 0.7359 (mmm) REVERT: C 1182 PHE cc_start: 0.7340 (m-80) cc_final: 0.6898 (m-80) REVERT: C 1190 MET cc_start: 0.6643 (ttt) cc_final: 0.5987 (ttt) REVERT: C 1198 TYR cc_start: 0.7209 (t80) cc_final: 0.6751 (t80) REVERT: E 21 ILE cc_start: 0.8666 (mt) cc_final: 0.8373 (tp) REVERT: E 42 LEU cc_start: 0.6806 (tp) cc_final: 0.6593 (mt) REVERT: I 52 TRP cc_start: 0.6662 (OUTLIER) cc_final: 0.5659 (t-100) REVERT: I 103 LEU cc_start: 0.8916 (tp) cc_final: 0.8485 (tt) outliers start: 51 outliers final: 23 residues processed: 886 average time/residue: 0.4775 time to fit residues: 696.8183 Evaluate side-chains 853 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 824 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 235 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 315 optimal weight: 4.9990 chunk 369 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 345 optimal weight: 0.7980 chunk 283 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 184 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 410 GLN A 624 ASN A1064 GLN A1150 HIS L 50 GLN B 410 GLN B 594 ASN B 844 ASN B1150 HIS ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN C1064 GLN C1096 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.148022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121741 restraints weight = 56627.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126420 restraints weight = 29303.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.129659 restraints weight = 18000.002| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34413 Z= 0.126 Angle : 0.594 9.052 46959 Z= 0.306 Chirality : 0.046 0.346 5376 Planarity : 0.003 0.037 5952 Dihedral : 7.066 101.241 5592 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.61 % Allowed : 11.48 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.12), residues: 4176 helix: -0.13 (0.18), residues: 747 sheet: -0.52 (0.16), residues: 984 loop : -1.13 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 47 HIS 0.005 0.001 HIS A 552 PHE 0.022 0.001 PHE A 774 TYR 0.021 0.001 TYR B1093 ARG 0.004 0.000 ARG G 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 36) link_NAG-ASN : angle 2.03055 ( 108) link_BETA1-4 : bond 0.00353 ( 12) link_BETA1-4 : angle 1.08037 ( 36) hydrogen bonds : bond 0.04149 ( 1134) hydrogen bonds : angle 6.12809 ( 3411) SS BOND : bond 0.00354 ( 69) SS BOND : angle 1.21544 ( 138) covalent geometry : bond 0.00282 (34296) covalent geometry : angle 0.58348 (46677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 873 time to evaluate : 3.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8539 (mt) cc_final: 0.8275 (mt) REVERT: A 201 ARG cc_start: 0.7298 (ptm-80) cc_final: 0.6951 (ptm-80) REVERT: A 254 LEU cc_start: 0.6935 (tt) cc_final: 0.6715 (tt) REVERT: A 315 ASN cc_start: 0.7844 (p0) cc_final: 0.7418 (p0) REVERT: A 328 ARG cc_start: 0.7115 (mpt180) cc_final: 0.6636 (mpt180) REVERT: A 342 ASN cc_start: 0.8266 (t0) cc_final: 0.7434 (t0) REVERT: A 343 ASP cc_start: 0.7361 (t0) cc_final: 0.7079 (t0) REVERT: A 345 SER cc_start: 0.7874 (p) cc_final: 0.7304 (m) REVERT: A 375 SER cc_start: 0.7930 (t) cc_final: 0.7320 (m) REVERT: A 425 ASP cc_start: 0.7722 (t70) cc_final: 0.7230 (t0) REVERT: A 435 TYR cc_start: 0.7400 (p90) cc_final: 0.7154 (p90) REVERT: A 437 LEU cc_start: 0.7870 (mt) cc_final: 0.7541 (mt) REVERT: A 478 VAL cc_start: 0.8194 (p) cc_final: 0.7877 (m) REVERT: A 573 GLN cc_start: 0.7696 (mp10) cc_final: 0.7457 (mp10) REVERT: A 610 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8015 (pp) REVERT: A 626 ASP cc_start: 0.7036 (t0) cc_final: 0.6436 (t0) REVERT: A 663 ASP cc_start: 0.7388 (t70) cc_final: 0.6792 (t70) REVERT: A 808 GLN cc_start: 0.7129 (pt0) cc_final: 0.6604 (pt0) REVERT: A 832 GLN cc_start: 0.7843 (mm110) cc_final: 0.7477 (mm110) REVERT: A 923 PHE cc_start: 0.7816 (m-80) cc_final: 0.7561 (m-80) REVERT: A 1000 ASP cc_start: 0.7371 (t0) cc_final: 0.7066 (t0) REVERT: A 1005 ASN cc_start: 0.7619 (t0) cc_final: 0.7307 (t0) REVERT: A 1035 GLN cc_start: 0.8120 (tp40) cc_final: 0.7864 (tp40) REVERT: A 1060 SER cc_start: 0.8264 (t) cc_final: 0.7938 (t) REVERT: A 1065 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6027 (mt-10) REVERT: A 1076 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: A 1112 MET cc_start: 0.7680 (mmm) cc_final: 0.7311 (mmm) REVERT: A 1119 VAL cc_start: 0.7204 (OUTLIER) cc_final: 0.6896 (m) REVERT: A 1141 ASN cc_start: 0.8367 (t0) cc_final: 0.8160 (t0) REVERT: A 1177 PRO cc_start: 0.8050 (Cg_endo) cc_final: 0.7598 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7428 (m-80) cc_final: 0.6527 (m-80) REVERT: A 1190 MET cc_start: 0.7077 (ttt) cc_final: 0.6423 (ttt) REVERT: L 31 HIS cc_start: 0.7348 (t70) cc_final: 0.6969 (t-170) REVERT: H 52 TRP cc_start: 0.6870 (OUTLIER) cc_final: 0.6139 (t-100) REVERT: H 103 LEU cc_start: 0.9072 (tp) cc_final: 0.8267 (tt) REVERT: B 180 LEU cc_start: 0.8593 (mt) cc_final: 0.8376 (mt) REVERT: B 201 ARG cc_start: 0.7379 (ptm-80) cc_final: 0.7098 (ptm-80) REVERT: B 235 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7755 (mtmm) REVERT: B 259 LYS cc_start: 0.7834 (ptmt) cc_final: 0.7399 (ptmt) REVERT: B 312 TYR cc_start: 0.7870 (m-10) cc_final: 0.7619 (m-10) REVERT: B 344 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7797 (ttmm) REVERT: B 345 SER cc_start: 0.8139 (p) cc_final: 0.7747 (m) REVERT: B 418 GLN cc_start: 0.7850 (tt0) cc_final: 0.7593 (tt0) REVERT: B 423 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7734 (mmm-85) REVERT: B 478 VAL cc_start: 0.8236 (p) cc_final: 0.7964 (m) REVERT: B 662 ARG cc_start: 0.7838 (mtp-110) cc_final: 0.7626 (mtp-110) REVERT: B 668 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7462 (mtm-85) REVERT: B 670 PHE cc_start: 0.7859 (m-80) cc_final: 0.7518 (m-80) REVERT: B 689 SER cc_start: 0.7641 (t) cc_final: 0.7392 (t) REVERT: B 772 GLU cc_start: 0.7451 (tp30) cc_final: 0.6945 (tp30) REVERT: B 860 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7103 (mp10) REVERT: B 866 MET cc_start: 0.5910 (mmm) cc_final: 0.5632 (mtm) REVERT: B 923 PHE cc_start: 0.7809 (m-80) cc_final: 0.7530 (m-80) REVERT: B 951 LEU cc_start: 0.8854 (mm) cc_final: 0.8595 (mt) REVERT: B 957 GLU cc_start: 0.6627 (mm-30) cc_final: 0.6342 (mm-30) REVERT: B 958 ASN cc_start: 0.8179 (m110) cc_final: 0.7621 (m-40) REVERT: B 963 TYR cc_start: 0.8309 (m-10) cc_final: 0.7648 (m-80) REVERT: B 1033 LYS cc_start: 0.8562 (tppt) cc_final: 0.8320 (ttmm) REVERT: B 1051 GLN cc_start: 0.7408 (mp10) cc_final: 0.7094 (mp10) REVERT: B 1087 LEU cc_start: 0.8528 (mt) cc_final: 0.8116 (mt) REVERT: B 1091 ASN cc_start: 0.8026 (m110) cc_final: 0.7792 (m110) REVERT: B 1113 GLU cc_start: 0.7606 (tt0) cc_final: 0.7040 (tt0) REVERT: B 1139 VAL cc_start: 0.8605 (t) cc_final: 0.8202 (p) REVERT: B 1141 ASN cc_start: 0.8547 (t0) cc_final: 0.7906 (t0) REVERT: B 1182 PHE cc_start: 0.7471 (m-80) cc_final: 0.7037 (m-80) REVERT: B 1189 TRP cc_start: 0.8410 (m100) cc_final: 0.8070 (m100) REVERT: B 1190 MET cc_start: 0.7089 (ttm) cc_final: 0.6587 (ttt) REVERT: G 52 TRP cc_start: 0.6757 (OUTLIER) cc_final: 0.5873 (t-100) REVERT: G 102 TRP cc_start: 0.7705 (p-90) cc_final: 0.7333 (p-90) REVERT: G 103 LEU cc_start: 0.9155 (tp) cc_final: 0.8427 (tt) REVERT: C 180 LEU cc_start: 0.8601 (mt) cc_final: 0.8258 (mp) REVERT: C 235 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7620 (mtmm) REVERT: C 237 LEU cc_start: 0.8406 (tp) cc_final: 0.8092 (tp) REVERT: C 259 LYS cc_start: 0.7719 (ptmt) cc_final: 0.7395 (ptmt) REVERT: C 314 LEU cc_start: 0.8740 (mm) cc_final: 0.8511 (mp) REVERT: C 325 VAL cc_start: 0.7498 (p) cc_final: 0.7232 (m) REVERT: C 326 TYR cc_start: 0.7409 (t80) cc_final: 0.7027 (t80) REVERT: C 328 ARG cc_start: 0.7065 (mpt180) cc_final: 0.6557 (mpt180) REVERT: C 342 ASN cc_start: 0.8303 (t0) cc_final: 0.8094 (t0) REVERT: C 343 ASP cc_start: 0.6935 (t70) cc_final: 0.6698 (t70) REVERT: C 344 LYS cc_start: 0.7887 (ttpp) cc_final: 0.7580 (ttmm) REVERT: C 375 SER cc_start: 0.7617 (t) cc_final: 0.7297 (m) REVERT: C 422 TYR cc_start: 0.7366 (t80) cc_final: 0.7119 (t80) REVERT: C 425 ASP cc_start: 0.7611 (t70) cc_final: 0.7169 (t0) REVERT: C 435 TYR cc_start: 0.7481 (p90) cc_final: 0.7269 (p90) REVERT: C 460 GLU cc_start: 0.8118 (mp0) cc_final: 0.7911 (mp0) REVERT: C 478 VAL cc_start: 0.8273 (p) cc_final: 0.8051 (m) REVERT: C 662 ARG cc_start: 0.7752 (mtp-110) cc_final: 0.7331 (mtm110) REVERT: C 689 SER cc_start: 0.7365 (t) cc_final: 0.7119 (t) REVERT: C 699 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7590 (mtmm) REVERT: C 730 TYR cc_start: 0.6873 (p90) cc_final: 0.6537 (p90) REVERT: C 817 ASP cc_start: 0.6778 (t70) cc_final: 0.6539 (p0) REVERT: C 832 GLN cc_start: 0.8098 (mm110) cc_final: 0.7236 (mp10) REVERT: C 860 GLN cc_start: 0.7411 (mp10) cc_final: 0.6919 (mp10) REVERT: C 925 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7223 (mt-10) REVERT: C 959 GLN cc_start: 0.8374 (mt0) cc_final: 0.8129 (mt0) REVERT: C 1000 ASP cc_start: 0.7336 (t0) cc_final: 0.6802 (t0) REVERT: C 1005 ASN cc_start: 0.7462 (t0) cc_final: 0.7051 (t0) REVERT: C 1033 LYS cc_start: 0.8391 (tppt) cc_final: 0.8051 (ttmm) REVERT: C 1039 ASN cc_start: 0.8332 (t0) cc_final: 0.7963 (t0) REVERT: C 1112 MET cc_start: 0.7618 (mmm) cc_final: 0.7395 (mmm) REVERT: C 1113 GLU cc_start: 0.7732 (tt0) cc_final: 0.7416 (tt0) REVERT: C 1182 PHE cc_start: 0.7369 (m-80) cc_final: 0.6984 (m-80) REVERT: C 1190 MET cc_start: 0.6840 (ttt) cc_final: 0.6143 (ttt) REVERT: C 1198 TYR cc_start: 0.7097 (t80) cc_final: 0.6512 (t80) REVERT: E 21 ILE cc_start: 0.8663 (mt) cc_final: 0.8409 (tp) REVERT: I 103 LEU cc_start: 0.8950 (tp) cc_final: 0.8463 (tt) outliers start: 59 outliers final: 32 residues processed: 892 average time/residue: 0.4830 time to fit residues: 705.1286 Evaluate side-chains 881 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 843 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain I residue 87 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 270 optimal weight: 0.9990 chunk 282 optimal weight: 0.0040 chunk 75 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 417 optimal weight: 4.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 ASN A1064 GLN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN B 844 ASN B1091 ASN B1150 HIS ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 HIS ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 ASN C 844 ASN C1096 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.139492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112914 restraints weight = 56880.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117441 restraints weight = 29607.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120554 restraints weight = 18265.717| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 34413 Z= 0.235 Angle : 0.673 9.028 46959 Z= 0.351 Chirality : 0.048 0.357 5376 Planarity : 0.004 0.044 5952 Dihedral : 6.812 97.734 5592 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.54 % Allowed : 13.33 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 4176 helix: -0.05 (0.18), residues: 750 sheet: -0.72 (0.16), residues: 1017 loop : -1.11 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP I 102 HIS 0.009 0.002 HIS A 552 PHE 0.030 0.002 PHE C 399 TYR 0.025 0.002 TYR C1191 ARG 0.010 0.001 ARG A 991 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 36) link_NAG-ASN : angle 2.24180 ( 108) link_BETA1-4 : bond 0.00368 ( 12) link_BETA1-4 : angle 1.26063 ( 36) hydrogen bonds : bond 0.04494 ( 1134) hydrogen bonds : angle 5.99911 ( 3411) SS BOND : bond 0.00508 ( 69) SS BOND : angle 1.57490 ( 138) covalent geometry : bond 0.00517 (34296) covalent geometry : angle 0.66005 (46677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 885 time to evaluate : 4.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8625 (mt) cc_final: 0.8370 (mp) REVERT: A 280 GLN cc_start: 0.7242 (mm110) cc_final: 0.6685 (mm-40) REVERT: A 315 ASN cc_start: 0.7846 (p0) cc_final: 0.7475 (p0) REVERT: A 328 ARG cc_start: 0.7070 (mpt180) cc_final: 0.6475 (mpt180) REVERT: A 342 ASN cc_start: 0.8427 (t0) cc_final: 0.7660 (t0) REVERT: A 375 SER cc_start: 0.7884 (t) cc_final: 0.7309 (m) REVERT: A 425 ASP cc_start: 0.7783 (t70) cc_final: 0.7222 (t0) REVERT: A 435 TYR cc_start: 0.7405 (p90) cc_final: 0.7204 (p90) REVERT: A 437 LEU cc_start: 0.8059 (mt) cc_final: 0.7729 (mt) REVERT: A 478 VAL cc_start: 0.8217 (p) cc_final: 0.7974 (m) REVERT: A 596 ILE cc_start: 0.8534 (mm) cc_final: 0.8312 (mm) REVERT: A 626 ASP cc_start: 0.6917 (t0) cc_final: 0.6304 (t0) REVERT: A 663 ASP cc_start: 0.7626 (t70) cc_final: 0.7152 (t70) REVERT: A 699 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7993 (mtmm) REVERT: A 731 ASN cc_start: 0.7645 (t0) cc_final: 0.7325 (t0) REVERT: A 772 GLU cc_start: 0.7505 (tp30) cc_final: 0.7256 (tp30) REVERT: A 832 GLN cc_start: 0.7796 (mm110) cc_final: 0.7559 (mm110) REVERT: A 858 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7487 (mm-40) REVERT: A 957 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6637 (mm-30) REVERT: A 960 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8485 (m-80) REVERT: A 1000 ASP cc_start: 0.7544 (t0) cc_final: 0.7278 (t0) REVERT: A 1035 GLN cc_start: 0.8257 (tp40) cc_final: 0.8027 (tp40) REVERT: A 1039 ASN cc_start: 0.8513 (t0) cc_final: 0.8225 (t0) REVERT: A 1051 GLN cc_start: 0.7507 (mp10) cc_final: 0.7105 (mp10) REVERT: A 1060 SER cc_start: 0.8436 (t) cc_final: 0.8125 (t) REVERT: A 1065 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6219 (mt-10) REVERT: A 1076 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7172 (tt0) REVERT: A 1112 MET cc_start: 0.7728 (mmm) cc_final: 0.7522 (mmm) REVERT: A 1113 GLU cc_start: 0.7828 (tt0) cc_final: 0.7577 (mt-10) REVERT: A 1119 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.7096 (m) REVERT: A 1141 ASN cc_start: 0.8656 (t0) cc_final: 0.8085 (t0) REVERT: A 1177 PRO cc_start: 0.8139 (Cg_endo) cc_final: 0.7549 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7480 (m-80) cc_final: 0.6544 (m-80) REVERT: A 1190 MET cc_start: 0.7145 (ttt) cc_final: 0.6528 (ttt) REVERT: L 31 HIS cc_start: 0.7647 (t70) cc_final: 0.7059 (t-170) REVERT: L 78 LEU cc_start: 0.7989 (tp) cc_final: 0.7677 (tp) REVERT: H 47 TRP cc_start: 0.7364 (t60) cc_final: 0.6984 (t60) REVERT: H 52 TRP cc_start: 0.7062 (OUTLIER) cc_final: 0.6262 (t-100) REVERT: H 103 LEU cc_start: 0.9015 (tp) cc_final: 0.8122 (tt) REVERT: B 180 LEU cc_start: 0.8704 (mt) cc_final: 0.8451 (mt) REVERT: B 201 ARG cc_start: 0.7547 (ptm-80) cc_final: 0.6904 (ptm-80) REVERT: B 235 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7737 (mtmm) REVERT: B 259 LYS cc_start: 0.7812 (ptmt) cc_final: 0.7358 (ptmt) REVERT: B 312 TYR cc_start: 0.8024 (m-10) cc_final: 0.7701 (m-10) REVERT: B 326 TYR cc_start: 0.7524 (t80) cc_final: 0.7294 (t80) REVERT: B 328 ARG cc_start: 0.7477 (mpt180) cc_final: 0.6698 (mpt180) REVERT: B 329 LYS cc_start: 0.8210 (mttt) cc_final: 0.7968 (mmtt) REVERT: B 385 LYS cc_start: 0.7608 (ptpp) cc_final: 0.7394 (ptpp) REVERT: B 478 VAL cc_start: 0.8291 (p) cc_final: 0.8003 (m) REVERT: B 617 ILE cc_start: 0.8441 (mm) cc_final: 0.8000 (mm) REVERT: B 626 ASP cc_start: 0.7249 (t0) cc_final: 0.6284 (t0) REVERT: B 689 SER cc_start: 0.7635 (t) cc_final: 0.7288 (t) REVERT: B 697 ASN cc_start: 0.7991 (m110) cc_final: 0.7730 (m-40) REVERT: B 699 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7517 (mmmt) REVERT: B 772 GLU cc_start: 0.7613 (tp30) cc_final: 0.7091 (tp30) REVERT: B 803 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6902 (ttt) REVERT: B 866 MET cc_start: 0.6456 (mmm) cc_final: 0.6246 (mtm) REVERT: B 923 PHE cc_start: 0.7900 (m-80) cc_final: 0.7691 (m-80) REVERT: B 951 LEU cc_start: 0.8971 (mm) cc_final: 0.8738 (mt) REVERT: B 958 ASN cc_start: 0.8290 (m110) cc_final: 0.7776 (m-40) REVERT: B 963 TYR cc_start: 0.8384 (m-10) cc_final: 0.7655 (m-80) REVERT: B 1000 ASP cc_start: 0.7523 (t0) cc_final: 0.7222 (t0) REVERT: B 1051 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: B 1076 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: B 1080 ASP cc_start: 0.7403 (t0) cc_final: 0.6934 (t0) REVERT: B 1087 LEU cc_start: 0.8543 (mt) cc_final: 0.8018 (mt) REVERT: B 1091 ASN cc_start: 0.8174 (m-40) cc_final: 0.7932 (m110) REVERT: B 1112 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6845 (mpp) REVERT: B 1139 VAL cc_start: 0.8571 (t) cc_final: 0.8197 (p) REVERT: B 1141 ASN cc_start: 0.8531 (t0) cc_final: 0.7997 (t0) REVERT: B 1182 PHE cc_start: 0.7640 (m-80) cc_final: 0.7065 (m-80) REVERT: B 1189 TRP cc_start: 0.8469 (m100) cc_final: 0.8201 (m100) REVERT: B 1190 MET cc_start: 0.7135 (ttm) cc_final: 0.6573 (ttt) REVERT: D 75 ASP cc_start: 0.7796 (p0) cc_final: 0.6812 (m-30) REVERT: G 52 TRP cc_start: 0.6797 (OUTLIER) cc_final: 0.5720 (t-100) REVERT: G 60 TYR cc_start: 0.7579 (m-80) cc_final: 0.7211 (m-80) REVERT: G 103 LEU cc_start: 0.9046 (tp) cc_final: 0.8729 (tp) REVERT: C 180 LEU cc_start: 0.8713 (mt) cc_final: 0.8334 (mp) REVERT: C 227 PHE cc_start: 0.7155 (t80) cc_final: 0.6949 (t80) REVERT: C 235 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7576 (mtmm) REVERT: C 237 LEU cc_start: 0.8457 (tp) cc_final: 0.8105 (tp) REVERT: C 259 LYS cc_start: 0.7748 (ptmt) cc_final: 0.7407 (ptmt) REVERT: C 293 ASP cc_start: 0.7491 (m-30) cc_final: 0.7219 (m-30) REVERT: C 312 TYR cc_start: 0.7763 (m-10) cc_final: 0.7421 (m-10) REVERT: C 314 LEU cc_start: 0.8700 (mm) cc_final: 0.8417 (mp) REVERT: C 325 VAL cc_start: 0.7544 (p) cc_final: 0.7262 (m) REVERT: C 342 ASN cc_start: 0.8487 (t0) cc_final: 0.8165 (t0) REVERT: C 343 ASP cc_start: 0.7150 (t70) cc_final: 0.6794 (t70) REVERT: C 344 LYS cc_start: 0.7888 (ttpp) cc_final: 0.7548 (ttmm) REVERT: C 425 ASP cc_start: 0.7708 (t70) cc_final: 0.7143 (t0) REVERT: C 460 GLU cc_start: 0.8230 (mp0) cc_final: 0.7890 (mp0) REVERT: C 478 VAL cc_start: 0.8218 (p) cc_final: 0.8007 (m) REVERT: C 662 ARG cc_start: 0.7906 (mtp-110) cc_final: 0.7544 (mtm110) REVERT: C 663 ASP cc_start: 0.7509 (t70) cc_final: 0.6969 (t0) REVERT: C 680 VAL cc_start: 0.8262 (t) cc_final: 0.8005 (m) REVERT: C 689 SER cc_start: 0.7397 (t) cc_final: 0.7142 (t) REVERT: C 699 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7772 (mtmm) REVERT: C 730 TYR cc_start: 0.6963 (p90) cc_final: 0.6503 (p90) REVERT: C 774 PHE cc_start: 0.7462 (m-80) cc_final: 0.7235 (m-80) REVERT: C 832 GLN cc_start: 0.8084 (mm110) cc_final: 0.7325 (mp10) REVERT: C 925 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7292 (mt-10) REVERT: C 959 GLN cc_start: 0.8547 (mt0) cc_final: 0.8200 (mt0) REVERT: C 1005 ASN cc_start: 0.7772 (t0) cc_final: 0.7272 (t0) REVERT: C 1039 ASN cc_start: 0.8430 (t0) cc_final: 0.8040 (t0) REVERT: C 1065 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6816 (mt-10) REVERT: C 1113 GLU cc_start: 0.7951 (tt0) cc_final: 0.7584 (tt0) REVERT: C 1177 PRO cc_start: 0.8204 (Cg_endo) cc_final: 0.7614 (Cg_exo) REVERT: C 1182 PHE cc_start: 0.7452 (m-80) cc_final: 0.6676 (m-80) REVERT: C 1190 MET cc_start: 0.7027 (ttt) cc_final: 0.6601 (ttt) REVERT: E 21 ILE cc_start: 0.8653 (mt) cc_final: 0.8357 (tp) REVERT: E 54 TYR cc_start: 0.7384 (p90) cc_final: 0.7096 (p90) REVERT: E 84 GLU cc_start: 0.6804 (pp20) cc_final: 0.6450 (pp20) REVERT: I 103 LEU cc_start: 0.8958 (tp) cc_final: 0.8377 (tt) outliers start: 93 outliers final: 52 residues processed: 918 average time/residue: 0.5881 time to fit residues: 918.8970 Evaluate side-chains 904 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 843 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1051 GLN Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 954 LEU Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 344 optimal weight: 2.9990 chunk 372 optimal weight: 7.9990 chunk 327 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 273 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 256 optimal weight: 50.0000 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 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN A1064 GLN A1096 GLN A1187 ASN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS B 315 ASN B 410 GLN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN B1014 ASN B1150 HIS ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN C 844 ASN C1014 ASN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.113162 restraints weight = 56626.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117865 restraints weight = 28788.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121090 restraints weight = 17603.468| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 34413 Z= 0.204 Angle : 0.665 10.443 46959 Z= 0.344 Chirality : 0.048 0.347 5376 Planarity : 0.004 0.049 5952 Dihedral : 6.534 94.151 5592 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.81 % Allowed : 15.96 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 4176 helix: 0.20 (0.18), residues: 726 sheet: -0.75 (0.16), residues: 1017 loop : -1.12 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 102 HIS 0.007 0.001 HIS B 215 PHE 0.031 0.002 PHE A 420 TYR 0.023 0.002 TYR B 435 ARG 0.004 0.000 ARG A 991 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 36) link_NAG-ASN : angle 2.16296 ( 108) link_BETA1-4 : bond 0.00282 ( 12) link_BETA1-4 : angle 1.11305 ( 36) hydrogen bonds : bond 0.04250 ( 1134) hydrogen bonds : angle 5.90164 ( 3411) SS BOND : bond 0.00504 ( 69) SS BOND : angle 1.98906 ( 138) covalent geometry : bond 0.00453 (34296) covalent geometry : angle 0.64952 (46677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 892 time to evaluate : 4.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 TYR cc_start: 0.8321 (m-80) cc_final: 0.7893 (m-10) REVERT: A 180 LEU cc_start: 0.8653 (mt) cc_final: 0.8371 (mt) REVERT: A 203 PHE cc_start: 0.8292 (m-80) cc_final: 0.8083 (m-10) REVERT: A 235 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7455 (mtmm) REVERT: A 240 VAL cc_start: 0.8830 (t) cc_final: 0.8555 (p) REVERT: A 280 GLN cc_start: 0.7287 (mm110) cc_final: 0.6742 (mm-40) REVERT: A 315 ASN cc_start: 0.7879 (p0) cc_final: 0.7364 (p0) REVERT: A 342 ASN cc_start: 0.8406 (t0) cc_final: 0.7646 (t0) REVERT: A 362 PHE cc_start: 0.7917 (p90) cc_final: 0.7413 (p90) REVERT: A 375 SER cc_start: 0.7838 (t) cc_final: 0.7275 (m) REVERT: A 425 ASP cc_start: 0.7788 (t70) cc_final: 0.7275 (t0) REVERT: A 437 LEU cc_start: 0.8057 (mt) cc_final: 0.7636 (mt) REVERT: A 448 ASN cc_start: 0.8740 (t0) cc_final: 0.8407 (t0) REVERT: A 478 VAL cc_start: 0.8171 (p) cc_final: 0.7937 (m) REVERT: A 573 GLN cc_start: 0.7873 (mp10) cc_final: 0.7637 (mp10) REVERT: A 596 ILE cc_start: 0.8467 (mm) cc_final: 0.8240 (mt) REVERT: A 626 ASP cc_start: 0.6876 (t0) cc_final: 0.6275 (t0) REVERT: A 699 LYS cc_start: 0.8265 (mmmt) cc_final: 0.8049 (mtmm) REVERT: A 731 ASN cc_start: 0.7644 (t0) cc_final: 0.7317 (t0) REVERT: A 858 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7507 (mm-40) REVERT: A 1035 GLN cc_start: 0.8202 (tp40) cc_final: 0.7955 (tp40) REVERT: A 1051 GLN cc_start: 0.7528 (mp10) cc_final: 0.7025 (mp10) REVERT: A 1060 SER cc_start: 0.8403 (t) cc_final: 0.8200 (t) REVERT: A 1065 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6374 (mt-10) REVERT: A 1076 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: A 1112 MET cc_start: 0.7740 (mmm) cc_final: 0.7282 (mmm) REVERT: A 1113 GLU cc_start: 0.7849 (tt0) cc_final: 0.7593 (mt-10) REVERT: A 1141 ASN cc_start: 0.8663 (t0) cc_final: 0.8179 (t0) REVERT: A 1147 TYR cc_start: 0.7996 (t80) cc_final: 0.7629 (t80) REVERT: A 1158 TYR cc_start: 0.8308 (m-10) cc_final: 0.7943 (m-80) REVERT: A 1177 PRO cc_start: 0.8091 (Cg_endo) cc_final: 0.7515 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7441 (m-80) cc_final: 0.6412 (m-80) REVERT: A 1190 MET cc_start: 0.7157 (ttt) cc_final: 0.6672 (ttt) REVERT: L 31 HIS cc_start: 0.7692 (t70) cc_final: 0.6994 (t-170) REVERT: L 78 LEU cc_start: 0.7876 (tp) cc_final: 0.7661 (tp) REVERT: H 52 TRP cc_start: 0.6980 (OUTLIER) cc_final: 0.6095 (t-100) REVERT: H 103 LEU cc_start: 0.8961 (tp) cc_final: 0.8198 (tt) REVERT: B 29 LYS cc_start: 0.7749 (tptt) cc_final: 0.7303 (tppt) REVERT: B 180 LEU cc_start: 0.8769 (mt) cc_final: 0.8481 (mt) REVERT: B 235 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7723 (mtmm) REVERT: B 237 LEU cc_start: 0.8644 (tp) cc_final: 0.8321 (tt) REVERT: B 259 LYS cc_start: 0.7757 (ptmt) cc_final: 0.7300 (ptmt) REVERT: B 312 TYR cc_start: 0.8072 (m-10) cc_final: 0.7797 (m-10) REVERT: B 328 ARG cc_start: 0.7401 (mpt180) cc_final: 0.6520 (mpt180) REVERT: B 329 LYS cc_start: 0.8317 (mttt) cc_final: 0.8070 (mmtt) REVERT: B 478 VAL cc_start: 0.8218 (p) cc_final: 0.7982 (m) REVERT: B 610 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8183 (pp) REVERT: B 626 ASP cc_start: 0.7162 (t0) cc_final: 0.6325 (t0) REVERT: B 662 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7701 (mtp-110) REVERT: B 689 SER cc_start: 0.7563 (t) cc_final: 0.7280 (t) REVERT: B 697 ASN cc_start: 0.7931 (m110) cc_final: 0.7596 (m-40) REVERT: B 772 GLU cc_start: 0.7718 (tp30) cc_final: 0.7114 (tp30) REVERT: B 803 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6857 (ttt) REVERT: B 833 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7270 (tt) REVERT: B 923 PHE cc_start: 0.7817 (m-80) cc_final: 0.7599 (m-80) REVERT: B 951 LEU cc_start: 0.8972 (mm) cc_final: 0.8732 (mt) REVERT: B 958 ASN cc_start: 0.8297 (m110) cc_final: 0.7787 (m-40) REVERT: B 1000 ASP cc_start: 0.7402 (t0) cc_final: 0.7123 (t0) REVERT: B 1051 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6999 (mp10) REVERT: B 1080 ASP cc_start: 0.7474 (t0) cc_final: 0.6976 (t0) REVERT: B 1087 LEU cc_start: 0.8637 (mt) cc_final: 0.8148 (mt) REVERT: B 1112 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6872 (mpp) REVERT: B 1139 VAL cc_start: 0.8553 (t) cc_final: 0.8140 (p) REVERT: B 1141 ASN cc_start: 0.8570 (t0) cc_final: 0.8024 (t0) REVERT: B 1181 TYR cc_start: 0.7739 (m-80) cc_final: 0.7457 (m-10) REVERT: B 1182 PHE cc_start: 0.7625 (m-80) cc_final: 0.7096 (m-80) REVERT: B 1189 TRP cc_start: 0.8483 (m100) cc_final: 0.8176 (m100) REVERT: B 1190 MET cc_start: 0.7163 (ttm) cc_final: 0.6600 (ttt) REVERT: G 52 TRP cc_start: 0.6779 (OUTLIER) cc_final: 0.5766 (t-100) REVERT: G 102 TRP cc_start: 0.7810 (p-90) cc_final: 0.7278 (p-90) REVERT: G 103 LEU cc_start: 0.9021 (tp) cc_final: 0.8656 (tp) REVERT: C 180 LEU cc_start: 0.8720 (mt) cc_final: 0.8329 (mp) REVERT: C 198 LEU cc_start: 0.8374 (mt) cc_final: 0.8137 (mt) REVERT: C 235 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7554 (mtmm) REVERT: C 237 LEU cc_start: 0.8443 (tp) cc_final: 0.8071 (tp) REVERT: C 259 LYS cc_start: 0.7763 (ptmt) cc_final: 0.7469 (ptmt) REVERT: C 293 ASP cc_start: 0.7409 (m-30) cc_final: 0.7188 (m-30) REVERT: C 312 TYR cc_start: 0.7772 (m-10) cc_final: 0.7352 (m-10) REVERT: C 317 TYR cc_start: 0.6198 (t80) cc_final: 0.5977 (t80) REVERT: C 325 VAL cc_start: 0.7544 (p) cc_final: 0.7239 (m) REVERT: C 326 TYR cc_start: 0.7474 (t80) cc_final: 0.7132 (t80) REVERT: C 328 ARG cc_start: 0.7099 (mpt180) cc_final: 0.6673 (mpt180) REVERT: C 342 ASN cc_start: 0.8476 (t0) cc_final: 0.8109 (t0) REVERT: C 343 ASP cc_start: 0.7184 (t70) cc_final: 0.6787 (t70) REVERT: C 344 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7560 (ttmm) REVERT: C 425 ASP cc_start: 0.7695 (t70) cc_final: 0.7136 (t0) REVERT: C 460 GLU cc_start: 0.8251 (mp0) cc_final: 0.7981 (mp0) REVERT: C 663 ASP cc_start: 0.7577 (t70) cc_final: 0.6872 (t0) REVERT: C 680 VAL cc_start: 0.8233 (t) cc_final: 0.8008 (m) REVERT: C 689 SER cc_start: 0.7360 (t) cc_final: 0.7116 (t) REVERT: C 699 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7832 (mtmm) REVERT: C 730 TYR cc_start: 0.6944 (p90) cc_final: 0.6444 (p90) REVERT: C 817 ASP cc_start: 0.6950 (t70) cc_final: 0.6563 (p0) REVERT: C 832 GLN cc_start: 0.8035 (mm110) cc_final: 0.7258 (mp10) REVERT: C 921 VAL cc_start: 0.8044 (m) cc_final: 0.7441 (m) REVERT: C 925 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7270 (mt-10) REVERT: C 959 GLN cc_start: 0.8551 (mt0) cc_final: 0.8320 (mt0) REVERT: C 1005 ASN cc_start: 0.7841 (t0) cc_final: 0.7365 (t0) REVERT: C 1039 ASN cc_start: 0.8416 (t0) cc_final: 0.8027 (t0) REVERT: C 1065 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6815 (mt-10) REVERT: C 1073 LEU cc_start: 0.7900 (pt) cc_final: 0.7438 (pt) REVERT: C 1074 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7368 (mm-30) REVERT: C 1113 GLU cc_start: 0.8005 (tt0) cc_final: 0.7632 (tt0) REVERT: C 1141 ASN cc_start: 0.8686 (t0) cc_final: 0.8365 (m-40) REVERT: C 1182 PHE cc_start: 0.7478 (m-80) cc_final: 0.7046 (m-80) REVERT: C 1190 MET cc_start: 0.6943 (ttt) cc_final: 0.6439 (ttt) REVERT: E 21 ILE cc_start: 0.8636 (mt) cc_final: 0.8323 (tp) REVERT: E 54 TYR cc_start: 0.7396 (p90) cc_final: 0.7107 (p90) REVERT: I 103 LEU cc_start: 0.8911 (tp) cc_final: 0.8271 (tt) outliers start: 103 outliers final: 61 residues processed: 927 average time/residue: 0.5566 time to fit residues: 862.7317 Evaluate side-chains 922 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 853 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1051 GLN Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 71.8728 > 50: distance: 8 - 13: 27.206 distance: 13 - 14: 44.377 distance: 14 - 15: 38.624 distance: 14 - 17: 28.671 distance: 15 - 16: 56.018 distance: 15 - 21: 41.281 distance: 17 - 18: 28.077 distance: 18 - 19: 40.740 distance: 22 - 23: 69.828 distance: 22 - 25: 41.970 distance: 23 - 24: 57.352 distance: 23 - 29: 68.137 distance: 25 - 26: 39.584 distance: 26 - 27: 43.638 distance: 26 - 28: 45.441 distance: 29 - 30: 39.955 distance: 30 - 31: 39.900 distance: 31 - 36: 68.409 distance: 34 - 35: 40.780 distance: 36 - 37: 41.379 distance: 37 - 38: 39.980 distance: 37 - 40: 44.820 distance: 38 - 39: 42.671 distance: 38 - 44: 38.656 distance: 40 - 41: 17.633 distance: 41 - 42: 56.975 distance: 41 - 43: 56.022 distance: 44 - 45: 40.875 distance: 45 - 48: 40.793 distance: 46 - 50: 67.349 distance: 48 - 49: 43.781 distance: 49 - 146: 34.767 distance: 50 - 51: 57.263 distance: 51 - 52: 41.362 distance: 51 - 54: 68.859 distance: 52 - 58: 55.793 distance: 54 - 55: 57.691 distance: 55 - 56: 57.639 distance: 55 - 57: 55.427 distance: 58 - 59: 57.688 distance: 59 - 60: 69.538 distance: 59 - 62: 56.178 distance: 60 - 61: 56.909 distance: 60 - 66: 39.107 distance: 61 - 94: 35.638 distance: 62 - 63: 57.792 distance: 62 - 64: 40.401 distance: 63 - 65: 56.274 distance: 66 - 67: 39.672 distance: 67 - 70: 57.809 distance: 68 - 69: 40.788 distance: 68 - 75: 51.996 distance: 69 - 102: 32.423 distance: 70 - 71: 39.793 distance: 72 - 73: 29.790 distance: 72 - 74: 22.093 distance: 75 - 76: 24.718 distance: 76 - 77: 54.287 distance: 76 - 79: 45.706 distance: 77 - 78: 40.968 distance: 80 - 81: 55.417 distance: 82 - 94: 34.374 distance: 84 - 85: 40.963 distance: 85 - 86: 37.644 distance: 85 - 87: 41.323 distance: 86 - 88: 23.599 distance: 87 - 89: 60.386 distance: 88 - 89: 48.045 distance: 89 - 91: 44.967 distance: 90 - 92: 5.961 distance: 91 - 93: 9.365 distance: 92 - 93: 45.641