Starting phenix.real_space_refine on Mon Aug 25 21:31:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d0c_30530/08_2025/7d0c_30530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d0c_30530/08_2025/7d0c_30530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d0c_30530/08_2025/7d0c_30530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d0c_30530/08_2025/7d0c_30530.map" model { file = "/net/cci-nas-00/data/ceres_data/7d0c_30530/08_2025/7d0c_30530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d0c_30530/08_2025/7d0c_30530.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 129 5.16 5 C 19639 2.51 5 N 5068 2.21 5 O 6130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30966 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1640 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain: "L" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1647 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1640 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1647 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: "b" 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: "c" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 7.66, per 1000 atoms: 0.25 Number of scatterers: 30966 At special positions: 0 Unit cell: (134.788, 173.92, 236.966, 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 129 16.00 O 6130 8.00 N 5068 7.00 C 19639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.40 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.13 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.25 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.52 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=1.82 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.13 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=1.47 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.52 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 343 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 331 " " NAG U 1 " - " ASN C 343 " " NAG V 1 " - " ASN C 709 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " " NAG b 1 " - " ASN A 331 " " NAG c 1 " - " ASN B1074 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7204 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 66 sheets defined 19.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.815A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.865A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.646A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.641A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.815A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.865A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.582A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 188 Processing helix chain 'G' and resid 191 through 193 No H-bonds generated for 'chain 'G' and resid 191 through 193' Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.839A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.339A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.712A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.539A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.650A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.780A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.152A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.757A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS C 291 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.839A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.231A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.502A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.466A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS H 95 " --> pdb=" O TRP H 107 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TRP H 107 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG H 97 " --> pdb=" O ASP H 105 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.466A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR H 111 " --> pdb=" O TYR H 93 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.008A pdb=" N ALA H 141 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 188 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.008A pdb=" N ALA H 141 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 188 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 154 through 158 Processing sheet with id=AF7, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.194A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.137A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 115 through 119 Processing sheet with id=AG1, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AG2, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.502A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.466A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR G 33 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N CYS G 95 " --> pdb=" O TRP G 107 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TRP G 107 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG G 97 " --> pdb=" O ASP G 105 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.466A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR G 33 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR G 111 " --> pdb=" O TYR G 93 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 124 through 128 removed outlier: 5.008A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 124 through 128 removed outlier: 5.008A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 154 through 158 Processing sheet with id=AG9, first strand: chain 'F' and resid 5 through 6 removed outlier: 4.194A pdb=" N ASP F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.136A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 115 through 119 Processing sheet with id=AH3, first strand: chain 'F' and resid 154 through 155 1173 hydrogen bonds defined for protein. 3189 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.85 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9662 1.34 - 1.46: 8197 1.46 - 1.59: 13616 1.59 - 1.72: 0 1.72 - 1.85: 160 Bond restraints: 31635 Sorted by residual: bond pdb=" N PRO F 142 " pdb=" CD PRO F 142 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" N PRO L 142 " pdb=" CD PRO L 142 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" C THR C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.332 1.390 -0.058 1.34e-02 5.57e+03 1.87e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.067 1.59e-02 3.96e+03 1.77e+01 bond pdb=" N PRO C 521 " pdb=" CD PRO C 521 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.63e+01 ... (remaining 31630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 41907 2.70 - 5.39: 1015 5.39 - 8.09: 83 8.09 - 10.79: 9 10.79 - 13.48: 2 Bond angle restraints: 43016 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 angle pdb=" N GLU C 156 " pdb=" CA GLU C 156 " pdb=" C GLU C 156 " ideal model delta sigma weight residual 108.45 115.84 -7.39 1.26e+00 6.30e-01 3.44e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 119.78 114.03 5.75 1.03e+00 9.43e-01 3.12e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.42 107.04 6.38 1.17e+00 7.31e-01 2.98e+01 angle pdb=" N ILE A 468 " pdb=" CA ILE A 468 " pdb=" C ILE A 468 " ideal model delta sigma weight residual 113.42 107.07 6.35 1.17e+00 7.31e-01 2.95e+01 ... (remaining 43011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17085 17.92 - 35.85: 1913 35.85 - 53.77: 539 53.77 - 71.69: 183 71.69 - 89.62: 60 Dihedral angle restraints: 19780 sinusoidal: 8573 harmonic: 11207 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.19 80.81 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.61 73.39 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 19777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5073 0.328 - 0.656: 3 0.656 - 0.984: 5 0.984 - 1.313: 0 1.313 - 1.641: 2 Chirality restraints: 5083 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-02 2.50e+03 1.09e+03 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.73e+01 ... (remaining 5080 not shown) Planarity restraints: 5510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " -0.180 2.00e-02 2.50e+03 2.75e-01 9.45e+02 pdb=" CG ASN C 343 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " -0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " 0.483 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.317 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.097 2.00e-02 2.50e+03 1.41e-01 2.48e+02 pdb=" CG ASN A 343 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.246 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.017 2.00e-02 2.50e+03 4.02e-02 2.02e+01 pdb=" CG ASN A 331 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.072 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.044 2.00e-02 2.50e+03 ... (remaining 5507 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 305 2.55 - 3.14: 23733 3.14 - 3.72: 46797 3.72 - 4.31: 67688 4.31 - 4.90: 110715 Nonbonded interactions: 249238 Sorted by model distance: nonbonded pdb=" O ILE A 233 " pdb=" O ASN A 234 " model vdw 1.962 3.040 nonbonded pdb=" O ASN L 138 " pdb=" O ASN L 139 " model vdw 2.038 3.040 nonbonded pdb=" O ASN F 138 " pdb=" O ASN F 139 " model vdw 2.039 3.040 nonbonded pdb=" OD1 ASN C 532 " pdb=" N LEU C 533 " model vdw 2.116 3.120 nonbonded pdb=" O SER A 813 " pdb=" OG SER A 813 " model vdw 2.183 3.040 ... (remaining 249233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 620 or resid 641 through 939 or resid 944 through 14 \ 10)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1408)) selection = (chain 'C' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 826 or resid 855 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' 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' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.780 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.561 31751 Z= 0.522 Angle : 1.316 66.918 43318 Z= 0.675 Chirality : 0.073 1.641 5083 Planarity : 0.007 0.083 5462 Dihedral : 17.370 89.617 12438 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 1.37 % Allowed : 8.86 % Favored : 89.77 % Rotamer: Outliers : 10.05 % Allowed : 17.31 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.67 (0.11), residues: 3792 helix: -2.16 (0.16), residues: 671 sheet: -1.54 (0.14), residues: 1067 loop : -3.12 (0.11), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1039 TYR 0.027 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.003 TRP A 104 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00960 (31635) covalent geometry : angle 1.02008 (43016) SS BOND : bond 0.15162 ( 46) SS BOND : angle 11.83739 ( 92) hydrogen bonds : bond 0.20376 ( 1095) hydrogen bonds : angle 8.37750 ( 3189) link_BETA1-4 : bond 0.05381 ( 22) link_BETA1-4 : angle 8.99109 ( 66) link_NAG-ASN : bond 0.02369 ( 48) link_NAG-ASN : angle 9.14459 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 338 poor density : 410 time to evaluate : 0.876 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 153 MET cc_start: 0.2041 (mpp) cc_final: -0.0475 (ptt) REVERT: A 517 LEU cc_start: 0.4881 (OUTLIER) cc_final: 0.4389 (tt) REVERT: A 532 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.6254 (m-40) REVERT: A 692 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8639 (mm) REVERT: A 698 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8694 (p) REVERT: A 984 LEU cc_start: 0.7316 (mt) cc_final: 0.6922 (mt) REVERT: B 284 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7767 (t) REVERT: B 569 ILE cc_start: 0.5385 (OUTLIER) cc_final: 0.4790 (mm) REVERT: C 86 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7357 (t80) REVERT: C 555 SER cc_start: 0.7036 (OUTLIER) cc_final: 0.6373 (m) REVERT: C 902 MET cc_start: 0.8516 (tpt) cc_final: 0.8296 (mmt) REVERT: C 1050 MET cc_start: 0.8823 (ptm) cc_final: 0.8612 (ptp) REVERT: H 167 VAL cc_start: 0.2355 (t) cc_final: 0.1841 (p) REVERT: L 33 TYR cc_start: 0.5723 (m-80) cc_final: 0.5095 (m-80) REVERT: L 36 TRP cc_start: 0.1184 (m100) cc_final: 0.0790 (m100) REVERT: L 40 LYS cc_start: 0.2280 (mmtt) cc_final: 0.1830 (tptm) REVERT: L 177 SER cc_start: 0.1012 (OUTLIER) cc_final: 0.0365 (t) REVERT: G 103 TYR cc_start: 0.1044 (t80) cc_final: 0.0607 (t80) REVERT: G 160 SER cc_start: -0.2699 (OUTLIER) cc_final: -0.3165 (t) REVERT: F 1 GLU cc_start: 0.4263 (tm-30) cc_final: 0.4006 (pm20) outliers start: 338 outliers final: 75 residues processed: 703 average time/residue: 0.1759 time to fit residues: 199.3859 Evaluate side-chains 267 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 182 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 40.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 134 GLN A 137 ASN A 188 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 690 GLN A 703 ASN A 762 GLN A 856 ASN A 901 GLN A 913 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 957 GLN A 969 ASN A 992 GLN B 115 GLN B 134 GLN B 188 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 540 ASN B 563 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B1054 GLN C 49 HIS C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 134 GLN C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 321 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 641 ASN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 954 GLN C 957 GLN C 969 ASN C 992 GLN C1010 GLN C1071 GLN C1101 HIS H 109 GLN H 168 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN G 32 ASN G 109 GLN G 168 HIS G 175 GLN F 39 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.157092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099596 restraints weight = 68052.728| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.66 r_work: 0.3090 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31751 Z= 0.175 Angle : 0.810 14.899 43318 Z= 0.394 Chirality : 0.051 0.469 5083 Planarity : 0.005 0.061 5462 Dihedral : 9.524 59.814 5732 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.12 % Favored : 92.62 % Rotamer: Outliers : 4.49 % Allowed : 19.39 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.12), residues: 3792 helix: -0.17 (0.19), residues: 699 sheet: -0.92 (0.15), residues: 1074 loop : -2.63 (0.12), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 109 TYR 0.027 0.002 TYR C 365 PHE 0.022 0.002 PHE B 133 TRP 0.012 0.001 TRP F 36 HIS 0.007 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00395 (31635) covalent geometry : angle 0.76527 (43016) SS BOND : bond 0.00425 ( 46) SS BOND : angle 1.64841 ( 92) hydrogen bonds : bond 0.04820 ( 1095) hydrogen bonds : angle 6.14189 ( 3189) link_BETA1-4 : bond 0.00685 ( 22) link_BETA1-4 : angle 2.53015 ( 66) link_NAG-ASN : bond 0.01250 ( 48) link_NAG-ASN : angle 4.19793 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 208 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1242 (mpp) cc_final: -0.0581 (ptp) REVERT: A 195 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7381 (mtmt) REVERT: A 532 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.6998 (m-40) REVERT: A 654 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8506 (mm-30) REVERT: A 856 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8360 (p0) REVERT: A 878 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 1092 GLU cc_start: 0.7916 (pp20) cc_final: 0.7703 (pp20) REVERT: B 200 TYR cc_start: 0.7198 (m-80) cc_final: 0.6941 (m-80) REVERT: B 403 ARG cc_start: 0.5212 (OUTLIER) cc_final: 0.4861 (ttm170) REVERT: B 473 TYR cc_start: 0.3577 (OUTLIER) cc_final: 0.2814 (t80) REVERT: B 569 ILE cc_start: 0.5645 (OUTLIER) cc_final: 0.5220 (mm) REVERT: B 614 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.7778 (t0) REVERT: B 740 MET cc_start: 0.8927 (tpp) cc_final: 0.8652 (tpp) REVERT: C 158 ARG cc_start: 0.3950 (tpt-90) cc_final: 0.2249 (mmp-170) REVERT: C 353 TRP cc_start: 0.4532 (p-90) cc_final: 0.4290 (p-90) REVERT: C 535 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8579 (mttt) REVERT: H 19 ARG cc_start: 0.4976 (tmm-80) cc_final: 0.4225 (tpt170) REVERT: H 109 GLN cc_start: 0.5294 (mm-40) cc_final: 0.5005 (pp30) REVERT: L 40 LYS cc_start: 0.3129 (mmtt) cc_final: 0.2481 (tptm) REVERT: L 108 LYS cc_start: 0.2467 (OUTLIER) cc_final: 0.1904 (tptt) REVERT: L 146 LYS cc_start: 0.3289 (mttt) cc_final: 0.2685 (tppt) REVERT: G 134 SER cc_start: -0.0897 (OUTLIER) cc_final: -0.1393 (t) REVERT: F 1 GLU cc_start: 0.4243 (tm-30) cc_final: 0.3827 (pm20) outliers start: 151 outliers final: 72 residues processed: 350 average time/residue: 0.1571 time to fit residues: 91.9529 Evaluate side-chains 227 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 144 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain F residue 176 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 193 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 351 optimal weight: 40.0000 chunk 132 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 422 ASN B 703 ASN B 913 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 168 HIS F 138 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.155500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097386 restraints weight = 68574.528| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.40 r_work: 0.3079 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31751 Z= 0.149 Angle : 0.714 12.938 43318 Z= 0.347 Chirality : 0.048 0.464 5083 Planarity : 0.005 0.050 5462 Dihedral : 8.268 59.655 5665 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.67 % Favored : 93.14 % Rotamer: Outliers : 4.31 % Allowed : 19.99 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.13), residues: 3792 helix: 0.67 (0.20), residues: 695 sheet: -0.49 (0.15), residues: 1064 loop : -2.31 (0.12), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.030 0.001 TYR A 365 PHE 0.022 0.002 PHE C 92 TRP 0.017 0.001 TRP F 36 HIS 0.006 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00344 (31635) covalent geometry : angle 0.67635 (43016) SS BOND : bond 0.00368 ( 46) SS BOND : angle 1.58054 ( 92) hydrogen bonds : bond 0.04240 ( 1095) hydrogen bonds : angle 5.60071 ( 3189) link_BETA1-4 : bond 0.00501 ( 22) link_BETA1-4 : angle 2.35389 ( 66) link_NAG-ASN : bond 0.00613 ( 48) link_NAG-ASN : angle 3.54564 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 166 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1149 (mpp) cc_final: -0.1564 (mmt) REVERT: A 269 TYR cc_start: 0.7716 (m-10) cc_final: 0.7210 (m-10) REVERT: A 351 TYR cc_start: 0.6659 (p90) cc_final: 0.6032 (p90) REVERT: A 532 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.6693 (m-40) REVERT: A 856 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8379 (p0) REVERT: A 902 MET cc_start: 0.8966 (tpt) cc_final: 0.8697 (mmt) REVERT: A 988 GLU cc_start: 0.8739 (tp30) cc_final: 0.8412 (tp30) REVERT: A 1005 GLN cc_start: 0.8653 (tt0) cc_final: 0.8240 (mt0) REVERT: A 1092 GLU cc_start: 0.7773 (pp20) cc_final: 0.7539 (pp20) REVERT: A 1142 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8717 (tm-30) REVERT: B 473 TYR cc_start: 0.3468 (OUTLIER) cc_final: 0.2603 (t80) REVERT: B 569 ILE cc_start: 0.5817 (OUTLIER) cc_final: 0.5435 (mm) REVERT: B 614 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7843 (t0) REVERT: B 740 MET cc_start: 0.8926 (tpp) cc_final: 0.8680 (tpp) REVERT: B 780 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8348 (mm-30) REVERT: B 884 SER cc_start: 0.9661 (OUTLIER) cc_final: 0.9368 (p) REVERT: B 976 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8641 (p) REVERT: C 86 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.5963 (t80) REVERT: C 133 PHE cc_start: 0.6169 (m-80) cc_final: 0.5873 (m-80) REVERT: C 158 ARG cc_start: 0.4048 (tpt-90) cc_final: 0.1800 (mmp80) REVERT: C 170 TYR cc_start: 0.6186 (t80) cc_final: 0.5818 (t80) REVERT: C 233 ILE cc_start: 0.6927 (tp) cc_final: 0.6470 (tt) REVERT: C 902 MET cc_start: 0.9040 (tpt) cc_final: 0.8829 (mmt) REVERT: H 19 ARG cc_start: 0.5222 (tmm-80) cc_final: 0.4500 (tpt170) REVERT: H 69 ILE cc_start: 0.1647 (pt) cc_final: 0.1270 (tt) REVERT: H 109 GLN cc_start: 0.5186 (mm-40) cc_final: 0.4974 (pp30) REVERT: L 36 TRP cc_start: 0.1818 (m100) cc_final: 0.1570 (m100) REVERT: L 40 LYS cc_start: 0.2999 (mmtt) cc_final: 0.2197 (tptm) REVERT: L 108 LYS cc_start: 0.2197 (OUTLIER) cc_final: 0.1706 (tptt) REVERT: G 134 SER cc_start: -0.0788 (OUTLIER) cc_final: -0.1306 (t) REVERT: F 1 GLU cc_start: 0.3860 (tm-30) cc_final: 0.3589 (mt-10) REVERT: F 138 ASN cc_start: 0.1313 (OUTLIER) cc_final: 0.1074 (t0) outliers start: 145 outliers final: 82 residues processed: 303 average time/residue: 0.1569 time to fit residues: 80.6835 Evaluate side-chains 237 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 144 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 176 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 208 optimal weight: 20.0000 chunk 356 optimal weight: 0.0370 chunk 271 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 374 optimal weight: 30.0000 chunk 266 optimal weight: 0.8980 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 755 GLN A 856 ASN A1106 GLN B 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 164 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN G 168 HIS F 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.153697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096036 restraints weight = 67987.878| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.76 r_work: 0.3029 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31751 Z= 0.169 Angle : 0.699 12.446 43318 Z= 0.339 Chirality : 0.048 0.469 5083 Planarity : 0.004 0.049 5462 Dihedral : 7.744 59.741 5655 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.94 % Favored : 92.91 % Rotamer: Outliers : 4.43 % Allowed : 20.29 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.13), residues: 3792 helix: 1.17 (0.20), residues: 681 sheet: -0.30 (0.15), residues: 1074 loop : -2.19 (0.12), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 457 TYR 0.021 0.001 TYR G 52 PHE 0.021 0.001 PHE A 86 TRP 0.010 0.001 TRP F 36 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00401 (31635) covalent geometry : angle 0.66612 (43016) SS BOND : bond 0.00342 ( 46) SS BOND : angle 1.55125 ( 92) hydrogen bonds : bond 0.04191 ( 1095) hydrogen bonds : angle 5.43064 ( 3189) link_BETA1-4 : bond 0.00465 ( 22) link_BETA1-4 : angle 2.28942 ( 66) link_NAG-ASN : bond 0.00533 ( 48) link_NAG-ASN : angle 3.22096 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 160 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1442 (mpp) cc_final: -0.1490 (mmt) REVERT: A 269 TYR cc_start: 0.7388 (m-10) cc_final: 0.6785 (m-10) REVERT: A 357 ARG cc_start: 0.7094 (ttp80) cc_final: 0.6722 (ttp-170) REVERT: A 532 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.6740 (m-40) REVERT: A 856 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8326 (p0) REVERT: A 878 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8954 (tt) REVERT: A 1005 GLN cc_start: 0.8743 (tt0) cc_final: 0.8413 (tt0) REVERT: A 1092 GLU cc_start: 0.7922 (pp20) cc_final: 0.7710 (pp20) REVERT: A 1142 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8751 (tm-30) REVERT: B 52 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 473 TYR cc_start: 0.3212 (OUTLIER) cc_final: 0.2461 (t80) REVERT: B 569 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5442 (mm) REVERT: B 614 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7797 (t0) REVERT: B 740 MET cc_start: 0.8901 (tpp) cc_final: 0.8527 (tpp) REVERT: B 780 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8336 (mm-30) REVERT: B 884 SER cc_start: 0.9641 (OUTLIER) cc_final: 0.9372 (p) REVERT: C 86 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.6114 (t80) REVERT: C 133 PHE cc_start: 0.6411 (m-80) cc_final: 0.6004 (m-80) REVERT: C 153 MET cc_start: 0.4466 (ptp) cc_final: 0.3330 (ptm) REVERT: C 158 ARG cc_start: 0.3917 (tpt-90) cc_final: 0.3522 (ttt90) REVERT: C 233 ILE cc_start: 0.6797 (tp) cc_final: 0.6272 (tt) REVERT: C 353 TRP cc_start: 0.4564 (p-90) cc_final: 0.4349 (p-90) REVERT: C 558 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7702 (mmmt) REVERT: C 902 MET cc_start: 0.9124 (tpt) cc_final: 0.8919 (mmt) REVERT: H 19 ARG cc_start: 0.5042 (tmm-80) cc_final: 0.4395 (tpt170) REVERT: H 50 VAL cc_start: 0.3919 (OUTLIER) cc_final: 0.3653 (p) REVERT: H 69 ILE cc_start: 0.1758 (pt) cc_final: 0.1457 (tt) REVERT: H 109 GLN cc_start: 0.5186 (mm-40) cc_final: 0.4943 (pp30) REVERT: L 36 TRP cc_start: 0.1803 (m100) cc_final: 0.1562 (m100) REVERT: L 40 LYS cc_start: 0.2577 (mmtt) cc_final: 0.2114 (tptm) REVERT: L 108 LYS cc_start: 0.2367 (OUTLIER) cc_final: 0.1897 (tptt) REVERT: G 134 SER cc_start: -0.0892 (OUTLIER) cc_final: -0.1395 (t) outliers start: 149 outliers final: 92 residues processed: 302 average time/residue: 0.1515 time to fit residues: 77.6553 Evaluate side-chains 248 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 144 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 176 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 338 optimal weight: 50.0000 chunk 324 optimal weight: 10.0000 chunk 276 optimal weight: 0.5980 chunk 220 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 225 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 30 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 125 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 168 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.152833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.093773 restraints weight = 68190.210| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.42 r_work: 0.3032 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31751 Z= 0.159 Angle : 0.674 12.025 43318 Z= 0.327 Chirality : 0.047 0.539 5083 Planarity : 0.004 0.051 5462 Dihedral : 7.380 59.831 5652 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.33 % Favored : 93.49 % Rotamer: Outliers : 4.05 % Allowed : 21.18 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.13), residues: 3792 helix: 1.44 (0.21), residues: 672 sheet: -0.26 (0.15), residues: 1095 loop : -2.07 (0.12), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 97 TYR 0.020 0.001 TYR C 380 PHE 0.020 0.001 PHE G 170 TRP 0.033 0.001 TRP H 36 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00378 (31635) covalent geometry : angle 0.64415 (43016) SS BOND : bond 0.00399 ( 46) SS BOND : angle 1.56259 ( 92) hydrogen bonds : bond 0.04043 ( 1095) hydrogen bonds : angle 5.27329 ( 3189) link_BETA1-4 : bond 0.00480 ( 22) link_BETA1-4 : angle 2.23266 ( 66) link_NAG-ASN : bond 0.00466 ( 48) link_NAG-ASN : angle 2.97985 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 155 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1466 (mpp) cc_final: -0.1367 (mmt) REVERT: A 269 TYR cc_start: 0.7466 (m-10) cc_final: 0.6864 (m-80) REVERT: A 357 ARG cc_start: 0.7408 (ttp80) cc_final: 0.7120 (ttp-170) REVERT: A 517 LEU cc_start: 0.6776 (mm) cc_final: 0.6414 (tt) REVERT: A 532 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.6901 (m-40) REVERT: A 878 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9071 (tt) REVERT: A 1005 GLN cc_start: 0.9004 (tt0) cc_final: 0.8674 (tt0) REVERT: A 1142 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8792 (tm-30) REVERT: B 52 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8388 (tm-30) REVERT: B 87 ASN cc_start: 0.7415 (m-40) cc_final: 0.6012 (t0) REVERT: B 473 TYR cc_start: 0.3323 (OUTLIER) cc_final: 0.2641 (t80) REVERT: B 569 ILE cc_start: 0.5907 (OUTLIER) cc_final: 0.5499 (mm) REVERT: B 740 MET cc_start: 0.9009 (tpp) cc_final: 0.8675 (tpp) REVERT: B 780 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8560 (mm-30) REVERT: B 884 SER cc_start: 0.9695 (OUTLIER) cc_final: 0.9450 (p) REVERT: C 86 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.6009 (t80) REVERT: C 133 PHE cc_start: 0.6339 (m-80) cc_final: 0.5973 (m-80) REVERT: C 153 MET cc_start: 0.4608 (ptp) cc_final: 0.3604 (ptm) REVERT: C 158 ARG cc_start: 0.4250 (tpt-90) cc_final: 0.3380 (ttt90) REVERT: C 233 ILE cc_start: 0.6859 (tp) cc_final: 0.6332 (tt) REVERT: C 353 TRP cc_start: 0.4503 (p-90) cc_final: 0.4171 (p-90) REVERT: C 902 MET cc_start: 0.9251 (tpt) cc_final: 0.9047 (mmt) REVERT: C 985 ASP cc_start: 0.8570 (p0) cc_final: 0.8343 (p0) REVERT: H 19 ARG cc_start: 0.5184 (tmm-80) cc_final: 0.4405 (tpt170) REVERT: H 50 VAL cc_start: 0.4246 (OUTLIER) cc_final: 0.3995 (p) REVERT: H 69 ILE cc_start: 0.1912 (pt) cc_final: 0.1591 (tt) REVERT: H 201 ASN cc_start: 0.3295 (OUTLIER) cc_final: 0.3035 (t0) REVERT: L 36 TRP cc_start: 0.1911 (m100) cc_final: 0.1647 (m100) REVERT: G 33 TYR cc_start: 0.2345 (m-10) cc_final: 0.1684 (m-80) REVERT: G 34 MET cc_start: 0.4046 (tpt) cc_final: 0.3770 (mmm) REVERT: G 134 SER cc_start: -0.1470 (OUTLIER) cc_final: -0.2007 (t) outliers start: 136 outliers final: 95 residues processed: 284 average time/residue: 0.1550 time to fit residues: 75.7658 Evaluate side-chains 249 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 145 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 70 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 308 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 362 optimal weight: 30.0000 chunk 217 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A1101 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.149031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089887 restraints weight = 67107.277| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.31 r_work: 0.2968 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 31751 Z= 0.267 Angle : 0.780 12.506 43318 Z= 0.379 Chirality : 0.051 0.565 5083 Planarity : 0.005 0.056 5462 Dihedral : 7.757 59.247 5646 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer: Outliers : 4.37 % Allowed : 20.88 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.13), residues: 3792 helix: 1.12 (0.20), residues: 688 sheet: -0.40 (0.15), residues: 1104 loop : -2.11 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1039 TYR 0.025 0.002 TYR C 380 PHE 0.026 0.002 PHE A 86 TRP 0.035 0.002 TRP H 36 HIS 0.012 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00644 (31635) covalent geometry : angle 0.74939 (43016) SS BOND : bond 0.00696 ( 46) SS BOND : angle 1.80056 ( 92) hydrogen bonds : bond 0.05202 ( 1095) hydrogen bonds : angle 5.50128 ( 3189) link_BETA1-4 : bond 0.00423 ( 22) link_BETA1-4 : angle 2.48939 ( 66) link_NAG-ASN : bond 0.00595 ( 48) link_NAG-ASN : angle 3.18141 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 154 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8132 (t70) REVERT: A 153 MET cc_start: 0.1542 (mpp) cc_final: -0.1274 (mmt) REVERT: A 532 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7254 (m-40) REVERT: A 649 CYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8748 (t) REVERT: A 740 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8687 (ttp) REVERT: A 878 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9048 (tt) REVERT: A 1005 GLN cc_start: 0.9076 (tt0) cc_final: 0.8637 (tt0) REVERT: B 52 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8529 (tm-30) REVERT: B 87 ASN cc_start: 0.7319 (m-40) cc_final: 0.6212 (t0) REVERT: B 569 ILE cc_start: 0.5918 (OUTLIER) cc_final: 0.5546 (mm) REVERT: C 153 MET cc_start: 0.4577 (ptp) cc_final: 0.3324 (ptm) REVERT: C 982 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8556 (m) REVERT: H 98 ASP cc_start: 0.4906 (t70) cc_final: 0.4642 (m-30) REVERT: L 146 LYS cc_start: 0.3505 (mttt) cc_final: 0.2854 (tppt) REVERT: G 33 TYR cc_start: 0.2440 (m-10) cc_final: 0.2127 (m-80) REVERT: G 34 MET cc_start: 0.4398 (tpt) cc_final: 0.3872 (tmm) outliers start: 147 outliers final: 97 residues processed: 289 average time/residue: 0.1696 time to fit residues: 84.2915 Evaluate side-chains 236 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 132 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 378 optimal weight: 50.0000 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 349 optimal weight: 7.9990 chunk 370 optimal weight: 30.0000 chunk 282 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 304 optimal weight: 9.9990 chunk 249 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.149881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091267 restraints weight = 67385.793| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.51 r_work: 0.2986 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 31751 Z= 0.188 Angle : 0.714 19.213 43318 Z= 0.346 Chirality : 0.048 0.536 5083 Planarity : 0.004 0.056 5462 Dihedral : 7.411 59.597 5642 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 3.63 % Allowed : 22.01 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.13), residues: 3792 helix: 1.27 (0.21), residues: 686 sheet: -0.27 (0.15), residues: 1127 loop : -2.05 (0.12), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.024 0.001 TYR C 380 PHE 0.019 0.002 PHE A 86 TRP 0.027 0.001 TRP H 36 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00450 (31635) covalent geometry : angle 0.68051 (43016) SS BOND : bond 0.00633 ( 46) SS BOND : angle 2.49325 ( 92) hydrogen bonds : bond 0.04429 ( 1095) hydrogen bonds : angle 5.33923 ( 3189) link_BETA1-4 : bond 0.00558 ( 22) link_BETA1-4 : angle 2.28257 ( 66) link_NAG-ASN : bond 0.00456 ( 48) link_NAG-ASN : angle 2.92763 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 147 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7991 (t70) REVERT: A 153 MET cc_start: 0.1712 (OUTLIER) cc_final: 0.1331 (pmm) REVERT: A 532 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7175 (m-40) REVERT: A 558 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8466 (pttm) REVERT: A 878 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8954 (tt) REVERT: A 1005 GLN cc_start: 0.8829 (tt0) cc_final: 0.8438 (tt0) REVERT: B 52 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 87 ASN cc_start: 0.7124 (m-40) cc_final: 0.6196 (t0) REVERT: B 569 ILE cc_start: 0.5553 (OUTLIER) cc_final: 0.5184 (mm) REVERT: C 153 MET cc_start: 0.4586 (ptp) cc_final: 0.4082 (ptp) REVERT: C 158 ARG cc_start: 0.4359 (tpt-90) cc_final: 0.3438 (ttt90) REVERT: C 233 ILE cc_start: 0.6550 (tp) cc_final: 0.6087 (tt) REVERT: C 982 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8534 (m) REVERT: H 19 ARG cc_start: 0.4857 (tmm-80) cc_final: 0.4181 (tpt170) REVERT: H 82 MET cc_start: 0.1069 (ptp) cc_final: 0.0788 (ptp) REVERT: L 146 LYS cc_start: 0.3518 (mttt) cc_final: 0.2797 (tppt) REVERT: G 33 TYR cc_start: 0.2396 (m-10) cc_final: 0.2192 (m-80) REVERT: G 34 MET cc_start: 0.4379 (tpt) cc_final: 0.3687 (tmm) REVERT: G 134 SER cc_start: -0.2100 (OUTLIER) cc_final: -0.2614 (t) outliers start: 122 outliers final: 95 residues processed: 262 average time/residue: 0.1728 time to fit residues: 79.0308 Evaluate side-chains 241 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 138 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.3325 > 50: distance: 81 - 85: 6.439 distance: 85 - 86: 10.946 distance: 86 - 87: 11.120 distance: 86 - 89: 9.302 distance: 87 - 88: 19.118 distance: 87 - 93: 9.508 distance: 89 - 90: 9.174 distance: 90 - 91: 26.726 distance: 90 - 92: 15.985 distance: 93 - 94: 26.315 distance: 94 - 95: 21.378 distance: 94 - 97: 11.639 distance: 95 - 96: 15.320 distance: 95 - 100: 13.302 distance: 97 - 98: 14.494 distance: 97 - 99: 15.010 distance: 100 - 101: 8.836 distance: 101 - 102: 5.064 distance: 101 - 104: 6.165 distance: 102 - 103: 12.711 distance: 102 - 111: 5.448 distance: 104 - 105: 7.798 distance: 111 - 112: 11.838 distance: 112 - 113: 4.805 distance: 112 - 115: 14.670 distance: 113 - 114: 29.048 distance: 113 - 119: 16.471 distance: 115 - 116: 8.384 distance: 116 - 117: 5.768 distance: 116 - 118: 9.863 distance: 119 - 120: 13.952 distance: 120 - 121: 14.791 distance: 120 - 123: 9.227 distance: 121 - 122: 22.315 distance: 121 - 127: 11.746 distance: 123 - 124: 6.696 distance: 124 - 125: 4.056 distance: 124 - 126: 4.753 distance: 127 - 128: 6.501 distance: 127 - 133: 6.200 distance: 128 - 129: 7.624 distance: 128 - 131: 4.976 distance: 129 - 130: 8.779 distance: 129 - 134: 19.487 distance: 131 - 132: 6.604 distance: 132 - 133: 6.776 distance: 134 - 135: 11.324 distance: 135 - 136: 13.130 distance: 135 - 138: 13.422 distance: 136 - 137: 12.075 distance: 136 - 143: 4.942 distance: 138 - 139: 15.138 distance: 139 - 140: 10.307 distance: 140 - 141: 8.395 distance: 140 - 142: 8.595 distance: 143 - 144: 21.874 distance: 144 - 145: 37.142 distance: 145 - 146: 33.495 distance: 145 - 147: 38.722 distance: 147 - 148: 18.963 distance: 148 - 149: 21.070 distance: 148 - 151: 17.357 distance: 149 - 150: 12.446 distance: 149 - 158: 35.060 distance: 151 - 152: 9.748 distance: 152 - 153: 13.025 distance: 152 - 154: 10.335 distance: 153 - 155: 7.541 distance: 154 - 156: 12.335 distance: 155 - 157: 6.243 distance: 156 - 157: 5.526 distance: 158 - 159: 25.937 distance: 159 - 160: 19.061 distance: 159 - 162: 10.684 distance: 160 - 161: 21.338 distance: 160 - 164: 22.131 distance: 162 - 163: 19.070