Starting phenix.real_space_refine on Thu Jun 26 09:40:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtq_34263/06_2025/8gtq_34263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtq_34263/06_2025/8gtq_34263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gtq_34263/06_2025/8gtq_34263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtq_34263/06_2025/8gtq_34263.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtq_34263/06_2025/8gtq_34263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtq_34263/06_2025/8gtq_34263.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.089 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 135 5.16 5 C 19449 2.51 5 N 4980 2.21 5 O 5955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 1.71s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30519 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "M" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "J" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 24.35, per 1000 atoms: 0.80 Number of scatterers: 30519 At special positions: 0 Unit cell: (152.934, 157.242, 192.783, 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 135 16.00 O 5955 8.00 N 4980 7.00 C 19449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.11 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=1.89 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.99 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.26 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=1.97 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.17 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.10 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.08 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.56 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.98 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.08 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.91 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.10 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.99 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.26 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.97 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.17 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 A1409 " - " NAG A1410 " " NAG B1409 " - " NAG B1410 " " NAG C1409 " - " NAG C1410 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " NAG Q 3 " " 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 X 2 " - " NAG X 3 " " 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 d 1 " - " NAG d 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 282 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 616 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1074 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 282 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 616 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 282 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 709 " " NAG C1409 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 331 " " NAG Z 1 " - " ASN C 343 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C1134 " Time building additional restraints: 13.45 Conformation dependent library (CDL) restraints added in 6.1 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6996 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 57 sheets defined 19.3% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.531A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.918A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (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: 3.987A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.513A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.652A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.080A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.930A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.532A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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: 3.986A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.513A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.535A 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 295 through 304 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.532A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.653A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.986A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.591A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.563A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.853A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.562A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.853A pdb=" N ILE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.563A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.852A pdb=" N ILE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.076A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.815A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.012A 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 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.575A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.547A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (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 removed outlier: 3.695A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.815A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 670 through 674 removed outlier: 3.935A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.868A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.740A 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: 7.152A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.499A 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 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.012A 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 removed outlier: 3.504A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.504A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 310 through 317 removed outlier: 5.056A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.815A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 656 removed outlier: 6.110A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.747A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.944A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.693A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.547A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 655 through 660 removed outlier: 4.609A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 58 through 60 Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 7 removed outlier: 6.539A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.652A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'I' and resid 58 through 60 Processing sheet with id=AF7, first strand: chain 'M' and resid 4 through 7 removed outlier: 6.540A pdb=" N THR M 69 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N GLN M 27 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N SER M 67 " --> pdb=" O GLN M 27 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE M 29 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 11.484A pdb=" N SER M 65 " --> pdb=" O ILE M 29 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.652A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'J' and resid 58 through 60 Processing sheet with id=AG2, first strand: chain 'N' and resid 4 through 7 removed outlier: 6.539A pdb=" N THR N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N GLN N 27 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N SER N 67 " --> pdb=" O GLN N 27 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE N 29 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N SER N 65 " --> pdb=" O ILE N 29 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.652A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 1106 hydrogen bonds defined for protein. 2940 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: 29.56 Time building geometry restraints manager: 14.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4888 1.28 - 1.42: 8248 1.42 - 1.55: 17904 1.55 - 1.68: 13 1.68 - 1.81: 177 Bond restraints: 31230 Sorted by residual: bond pdb=" C GLY B 857 " pdb=" O GLY B 857 " ideal model delta sigma weight residual 1.237 1.153 0.084 1.31e-02 5.83e+03 4.10e+01 bond pdb=" CA LEU B 858 " pdb=" C LEU B 858 " ideal model delta sigma weight residual 1.523 1.444 0.080 1.34e-02 5.57e+03 3.54e+01 bond pdb=" C LEU B 858 " pdb=" O LEU B 858 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.26e-02 6.30e+03 3.47e+01 bond pdb=" C LEU B 858 " pdb=" N THR B 859 " ideal model delta sigma weight residual 1.332 1.267 0.066 1.40e-02 5.10e+03 2.21e+01 bond pdb=" N PRO B 561 " pdb=" CD PRO B 561 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.18e+01 ... (remaining 31225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 41406 2.74 - 5.48: 900 5.48 - 8.21: 118 8.21 - 10.95: 20 10.95 - 13.69: 12 Bond angle restraints: 42456 Sorted by residual: angle pdb=" N THR C 588 " pdb=" CA THR C 588 " pdb=" C THR C 588 " ideal model delta sigma weight residual 110.40 100.10 10.30 1.31e+00 5.83e-01 6.18e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 120.66 113.87 6.79 1.09e+00 8.42e-01 3.88e+01 angle pdb=" N THR B 588 " pdb=" CA THR B 588 " pdb=" C THR B 588 " ideal model delta sigma weight residual 110.39 103.14 7.25 1.30e+00 5.92e-01 3.11e+01 angle pdb=" N ASN M 53 " pdb=" CA ASN M 53 " pdb=" C ASN M 53 " ideal model delta sigma weight residual 107.98 118.45 -10.47 1.88e+00 2.83e-01 3.10e+01 angle pdb=" N ASN N 53 " pdb=" CA ASN N 53 " pdb=" C ASN N 53 " ideal model delta sigma weight residual 107.98 118.44 -10.46 1.88e+00 2.83e-01 3.09e+01 ... (remaining 42451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17754 17.93 - 35.86: 1336 35.86 - 53.79: 304 53.79 - 71.72: 77 71.72 - 89.65: 29 Dihedral angle restraints: 19500 sinusoidal: 8589 harmonic: 10911 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 157.32 -64.32 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 157.31 -64.31 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 157.29 -64.29 1 1.00e+01 1.00e-02 5.44e+01 ... (remaining 19497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.233: 4913 0.233 - 0.466: 20 0.466 - 0.699: 4 0.699 - 0.932: 0 0.932 - 1.164: 4 Chirality restraints: 4941 Sorted by residual: chirality pdb=" C1 NAG A1410 " pdb=" O4 NAG A1409 " pdb=" C2 NAG A1410 " pdb=" O5 NAG A1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.19e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.18e+03 chirality pdb=" C1 NAG C1410 " pdb=" O4 NAG C1409 " pdb=" C2 NAG C1410 " pdb=" O5 NAG C1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.17e+03 ... (remaining 4938 not shown) Planarity restraints: 5436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.061 2.00e-02 2.50e+03 8.55e-02 9.14e+01 pdb=" CG ASN A 603 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " 0.151 2.00e-02 2.50e+03 pdb=" C1 NAG A1405 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.073 2.00e-02 2.50e+03 8.05e-02 8.11e+01 pdb=" CG ASN C 331 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.128 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.051 2.00e-02 2.50e+03 6.82e-02 5.81e+01 pdb=" CG ASN B 331 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.117 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.078 2.00e-02 2.50e+03 ... (remaining 5433 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 194 2.50 - 3.10: 21461 3.10 - 3.70: 42262 3.70 - 4.30: 63610 4.30 - 4.90: 107130 Nonbonded interactions: 234657 Sorted by model distance: nonbonded pdb=" O SER C 530 " pdb=" OG1 THR C 531 " model vdw 1.900 3.040 nonbonded pdb=" O GLN B 690 " pdb=" OG SER B 691 " model vdw 1.938 3.040 nonbonded pdb=" O PRO B 527 " pdb=" NZ LYS B 528 " model vdw 1.951 3.120 nonbonded pdb=" O PRO A 322 " pdb=" OG1 THR A 323 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASN C 532 " pdb=" N LEU C 533 " model vdw 1.991 3.120 ... (remaining 234652 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.220 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 105.450 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.970 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: 0.020 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 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 0.472 31347 Z= 0.567 Angle : 1.260 48.965 42765 Z= 0.671 Chirality : 0.075 1.164 4941 Planarity : 0.007 0.107 5388 Dihedral : 13.564 89.655 12378 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 1.87 % Allowed : 7.34 % Favored : 90.79 % Rotamer: Outliers : 3.06 % Allowed : 6.74 % Favored : 90.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.12), residues: 3693 helix: -1.15 (0.17), residues: 643 sheet: -1.54 (0.15), residues: 1067 loop : -2.66 (0.11), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 436 HIS 0.009 0.001 HIS H 35 PHE 0.025 0.002 PHE B 86 TYR 0.024 0.002 TYR B 453 ARG 0.004 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.02959 ( 48) link_NAG-ASN : angle 9.24287 ( 144) link_BETA1-4 : bond 0.06542 ( 27) link_BETA1-4 : angle 5.60244 ( 81) hydrogen bonds : bond 0.20537 ( 1046) hydrogen bonds : angle 7.85653 ( 2940) SS BOND : bond 0.11200 ( 42) SS BOND : angle 8.72364 ( 84) covalent geometry : bond 0.00945 (31230) covalent geometry : angle 1.04834 (42456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 670 time to evaluate : 3.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7791 (p90) cc_final: 0.7571 (p90) REVERT: A 201 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7279 (t80) REVERT: B 695 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8214 (p90) REVERT: C 693 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8372 (pp) REVERT: C 904 TYR cc_start: 0.6381 (m-10) cc_final: 0.5905 (m-10) outliers start: 100 outliers final: 41 residues processed: 759 average time/residue: 0.4446 time to fit residues: 530.4691 Evaluate side-chains 387 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 343 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 561 PRO Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 102 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 337 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 164 ASN A 173 GLN A 207 HIS A 422 ASN A 450 ASN A 607 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 907 ASN B 87 ASN B 121 ASN B 164 ASN B 422 ASN B 450 ASN B 532 ASN B 607 GLN B 613 GLN B 690 GLN B 774 GLN C 81 ASN C 121 ASN C 164 ASN C 422 ASN C 450 ASN C 607 GLN C 613 GLN C 955 ASN H 35 HIS I 35 HIS I 82 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN N 38 GLN N 53 ASN N 79 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.187810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.119507 restraints weight = 48856.778| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.58 r_work: 0.3475 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31347 Z= 0.164 Angle : 0.766 15.796 42765 Z= 0.384 Chirality : 0.048 0.351 4941 Planarity : 0.006 0.121 5388 Dihedral : 7.740 62.595 5709 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.79 % Favored : 93.88 % Rotamer: Outliers : 3.12 % Allowed : 13.24 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 3693 helix: 0.41 (0.20), residues: 640 sheet: -1.08 (0.15), residues: 1047 loop : -2.22 (0.12), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 3 HIS 0.006 0.001 HIS C 207 PHE 0.021 0.002 PHE L 73 TYR 0.020 0.002 TYR C 170 ARG 0.015 0.001 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 48) link_NAG-ASN : angle 3.26267 ( 144) link_BETA1-4 : bond 0.00987 ( 27) link_BETA1-4 : angle 2.97085 ( 81) hydrogen bonds : bond 0.05106 ( 1046) hydrogen bonds : angle 5.71770 ( 2940) SS BOND : bond 0.00519 ( 42) SS BOND : angle 2.99483 ( 84) covalent geometry : bond 0.00369 (31230) covalent geometry : angle 0.72150 (42456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 397 time to evaluate : 3.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8209 (p90) cc_final: 0.7880 (p90) REVERT: A 233 ILE cc_start: 0.5969 (mm) cc_final: 0.5262 (pt) REVERT: A 328 ARG cc_start: 0.6993 (mmt90) cc_final: 0.6691 (ttm-80) REVERT: A 950 ASP cc_start: 0.7779 (m-30) cc_final: 0.7464 (p0) REVERT: B 287 ASP cc_start: 0.7913 (t70) cc_final: 0.7578 (t70) REVERT: B 321 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7197 (mm-40) REVERT: B 613 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7946 (mm-40) REVERT: B 697 MET cc_start: 0.7928 (ptm) cc_final: 0.7686 (ptt) REVERT: B 725 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6652 (mt-10) REVERT: B 759 PHE cc_start: 0.7466 (m-10) cc_final: 0.7233 (m-10) REVERT: B 779 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8104 (tp40) REVERT: B 790 LYS cc_start: 0.9107 (mttt) cc_final: 0.8781 (mttm) REVERT: B 854 LYS cc_start: 0.5976 (OUTLIER) cc_final: 0.5111 (UNCLASSIFIED) REVERT: C 237 ARG cc_start: 0.6735 (mtm180) cc_final: 0.6470 (mtm180) REVERT: C 314 GLN cc_start: 0.8556 (tt0) cc_final: 0.8259 (tm-30) REVERT: C 495 TYR cc_start: 0.1775 (OUTLIER) cc_final: 0.1198 (m-80) REVERT: C 544 ASN cc_start: 0.7311 (t0) cc_final: 0.7071 (p0) REVERT: C 613 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: C 725 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: C 902 MET cc_start: 0.8637 (mmm) cc_final: 0.8247 (tpt) REVERT: C 969 LYS cc_start: 0.8386 (ptmm) cc_final: 0.7739 (tmmt) REVERT: C 984 LEU cc_start: 0.7828 (tp) cc_final: 0.6654 (tp) REVERT: L 87 TYR cc_start: 0.7692 (m-80) cc_final: 0.7461 (m-80) REVERT: L 89 GLN cc_start: 0.7743 (tt0) cc_final: 0.7406 (pt0) REVERT: I 34 MET cc_start: 0.7914 (mmm) cc_final: 0.7679 (mmm) REVERT: I 83 MET cc_start: 0.5048 (mtm) cc_final: 0.4691 (mtt) REVERT: I 93 VAL cc_start: 0.6525 (t) cc_final: 0.6318 (p) REVERT: I 101 ASP cc_start: 0.7608 (t70) cc_final: 0.7373 (t0) REVERT: M 33 LEU cc_start: 0.9028 (tp) cc_final: 0.8710 (tp) REVERT: M 35 TRP cc_start: 0.6232 (m100) cc_final: 0.5984 (m100) REVERT: M 70 ASP cc_start: 0.8133 (p0) cc_final: 0.7634 (t70) REVERT: M 71 PHE cc_start: 0.7872 (m-10) cc_final: 0.7645 (m-10) REVERT: N 34 ASN cc_start: 0.8711 (m110) cc_final: 0.8337 (m-40) REVERT: N 36 TYR cc_start: 0.7732 (m-80) cc_final: 0.6694 (m-80) REVERT: N 46 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.4850 (tt) REVERT: N 62 PHE cc_start: 0.6858 (m-80) cc_final: 0.6628 (m-80) REVERT: N 87 TYR cc_start: 0.7676 (m-80) cc_final: 0.7319 (m-80) outliers start: 102 outliers final: 40 residues processed: 479 average time/residue: 0.4178 time to fit residues: 326.5439 Evaluate side-chains 364 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 316 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 360 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 310 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 364 optimal weight: 8.9990 chunk 296 optimal weight: 0.1980 chunk 27 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 ASN N 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.180041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.107909 restraints weight = 48153.918| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.55 r_work: 0.3308 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 31347 Z= 0.243 Angle : 0.755 12.882 42765 Z= 0.378 Chirality : 0.049 0.314 4941 Planarity : 0.005 0.106 5388 Dihedral : 6.471 54.798 5656 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.09 % Favored : 93.69 % Rotamer: Outliers : 3.16 % Allowed : 14.43 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3693 helix: 0.49 (0.20), residues: 660 sheet: -0.89 (0.15), residues: 1038 loop : -1.95 (0.12), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1102 HIS 0.032 0.002 HIS A 207 PHE 0.024 0.002 PHE C 86 TYR 0.018 0.002 TYR B 265 ARG 0.013 0.001 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 48) link_NAG-ASN : angle 2.96163 ( 144) link_BETA1-4 : bond 0.00749 ( 27) link_BETA1-4 : angle 2.73953 ( 81) hydrogen bonds : bond 0.04864 ( 1046) hydrogen bonds : angle 5.49550 ( 2940) SS BOND : bond 0.00662 ( 42) SS BOND : angle 2.89824 ( 84) covalent geometry : bond 0.00585 (31230) covalent geometry : angle 0.71672 (42456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 344 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8155 (p90) cc_final: 0.7885 (p90) REVERT: A 233 ILE cc_start: 0.6337 (OUTLIER) cc_final: 0.5771 (pt) REVERT: A 328 ARG cc_start: 0.6948 (mmt90) cc_final: 0.6497 (mmm-85) REVERT: A 558 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8414 (mmmt) REVERT: A 586 ASP cc_start: 0.7483 (m-30) cc_final: 0.7135 (m-30) REVERT: A 725 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: A 950 ASP cc_start: 0.7965 (m-30) cc_final: 0.7556 (p0) REVERT: A 984 LEU cc_start: 0.6760 (tp) cc_final: 0.6491 (tp) REVERT: B 153 MET cc_start: 0.3791 (ptm) cc_final: 0.3415 (tmm) REVERT: B 321 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7558 (mm-40) REVERT: B 613 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8228 (mm-40) REVERT: B 620 VAL cc_start: 0.7130 (t) cc_final: 0.6917 (t) REVERT: B 697 MET cc_start: 0.8372 (ptm) cc_final: 0.8023 (ptt) REVERT: B 759 PHE cc_start: 0.7642 (m-80) cc_final: 0.7284 (m-10) REVERT: B 790 LYS cc_start: 0.9166 (mttt) cc_final: 0.8866 (mttm) REVERT: B 917 TYR cc_start: 0.8881 (m-80) cc_final: 0.8630 (m-80) REVERT: B 961 THR cc_start: 0.8238 (t) cc_final: 0.7992 (p) REVERT: C 115 GLN cc_start: 0.5924 (mm110) cc_final: 0.5454 (mm-40) REVERT: C 558 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8230 (mmtm) REVERT: C 613 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8743 (mt0) REVERT: C 725 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: C 731 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8935 (ptt) REVERT: C 786 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7942 (mmmt) REVERT: C 869 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7637 (mtp) REVERT: C 896 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8567 (tt) REVERT: C 904 TYR cc_start: 0.7301 (m-10) cc_final: 0.6760 (m-10) REVERT: C 969 LYS cc_start: 0.8376 (ptmm) cc_final: 0.8102 (ttpt) REVERT: C 1001 LEU cc_start: 0.7490 (tp) cc_final: 0.7255 (tt) REVERT: C 1050 MET cc_start: 0.8652 (ptm) cc_final: 0.8371 (ptm) REVERT: L 87 TYR cc_start: 0.7727 (m-80) cc_final: 0.7383 (m-80) REVERT: L 89 GLN cc_start: 0.7836 (tt0) cc_final: 0.7599 (pt0) REVERT: I 13 GLN cc_start: 0.7950 (mp10) cc_final: 0.7746 (mp10) REVERT: M 33 LEU cc_start: 0.8839 (tp) cc_final: 0.8246 (tt) REVERT: M 35 TRP cc_start: 0.6803 (m100) cc_final: 0.6601 (m100) REVERT: M 70 ASP cc_start: 0.8253 (p0) cc_final: 0.7714 (t70) REVERT: J 91 THR cc_start: 0.7276 (OUTLIER) cc_final: 0.7032 (t) REVERT: N 34 ASN cc_start: 0.8705 (m110) cc_final: 0.8261 (m-40) REVERT: N 36 TYR cc_start: 0.7624 (m-80) cc_final: 0.6596 (m-80) REVERT: N 46 LEU cc_start: 0.5310 (OUTLIER) cc_final: 0.5056 (tt) REVERT: N 62 PHE cc_start: 0.6413 (m-80) cc_final: 0.6108 (m-80) outliers start: 103 outliers final: 49 residues processed: 418 average time/residue: 0.4235 time to fit residues: 288.9634 Evaluate side-chains 360 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 300 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 150 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 138 optimal weight: 0.2980 chunk 267 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 96 optimal weight: 0.0060 chunk 255 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN C 644 GLN C 755 GLN H 3 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN J 57 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.188102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117265 restraints weight = 48374.671| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.49 r_work: 0.3306 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31347 Z= 0.153 Angle : 0.650 11.495 42765 Z= 0.323 Chirality : 0.046 0.250 4941 Planarity : 0.004 0.056 5388 Dihedral : 5.907 59.415 5645 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.55 % Favored : 94.34 % Rotamer: Outliers : 2.70 % Allowed : 15.62 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 3693 helix: 0.83 (0.21), residues: 648 sheet: -0.64 (0.16), residues: 981 loop : -1.76 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 47 HIS 0.005 0.001 HIS A 207 PHE 0.025 0.001 PHE C 565 TYR 0.011 0.001 TYR B 741 ARG 0.014 0.001 ARG I 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 48) link_NAG-ASN : angle 2.51190 ( 144) link_BETA1-4 : bond 0.00818 ( 27) link_BETA1-4 : angle 2.50921 ( 81) hydrogen bonds : bond 0.04002 ( 1046) hydrogen bonds : angle 5.16081 ( 2940) SS BOND : bond 0.00365 ( 42) SS BOND : angle 2.28389 ( 84) covalent geometry : bond 0.00361 (31230) covalent geometry : angle 0.61755 (42456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 317 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8124 (p90) cc_final: 0.7837 (p90) REVERT: A 233 ILE cc_start: 0.6392 (mm) cc_final: 0.5924 (pt) REVERT: A 558 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8431 (mmmt) REVERT: A 586 ASP cc_start: 0.7538 (m-30) cc_final: 0.6838 (m-30) REVERT: A 737 ASP cc_start: 0.7845 (t0) cc_final: 0.7289 (t70) REVERT: A 869 MET cc_start: 0.8110 (mtt) cc_final: 0.7807 (mtt) REVERT: A 950 ASP cc_start: 0.7932 (m-30) cc_final: 0.7537 (p0) REVERT: B 221 SER cc_start: 0.9179 (OUTLIER) cc_final: 0.8920 (t) REVERT: B 321 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7710 (mm-40) REVERT: B 613 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8312 (mm-40) REVERT: B 697 MET cc_start: 0.8364 (ptm) cc_final: 0.7959 (ptt) REVERT: B 725 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7035 (mt-10) REVERT: C 115 GLN cc_start: 0.5865 (mm110) cc_final: 0.5231 (mm110) REVERT: C 495 TYR cc_start: 0.1796 (OUTLIER) cc_final: 0.1532 (m-80) REVERT: C 558 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8236 (mmtm) REVERT: C 565 PHE cc_start: 0.7165 (p90) cc_final: 0.6578 (p90) REVERT: C 725 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: C 786 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8131 (mmmt) REVERT: C 900 MET cc_start: 0.8258 (ttm) cc_final: 0.7860 (mtp) REVERT: C 904 TYR cc_start: 0.7197 (m-10) cc_final: 0.6875 (m-10) REVERT: C 969 LYS cc_start: 0.8335 (ptmm) cc_final: 0.7985 (ttmt) REVERT: C 1001 LEU cc_start: 0.7457 (tp) cc_final: 0.7199 (tt) REVERT: C 1050 MET cc_start: 0.8557 (ptm) cc_final: 0.8276 (ptm) REVERT: H 3 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: L 31 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6652 (p90) REVERT: L 87 TYR cc_start: 0.7714 (m-80) cc_final: 0.7325 (m-80) REVERT: I 13 GLN cc_start: 0.8018 (mp10) cc_final: 0.7756 (mp10) REVERT: I 114 GLN cc_start: 0.7917 (mm110) cc_final: 0.7132 (mp10) REVERT: M 4 MET cc_start: 0.5079 (pmm) cc_final: 0.4121 (ptp) REVERT: M 32 TYR cc_start: 0.7975 (m-80) cc_final: 0.7561 (m-80) REVERT: M 33 LEU cc_start: 0.8730 (tp) cc_final: 0.8102 (tt) REVERT: M 35 TRP cc_start: 0.6747 (m100) cc_final: 0.6489 (m100) REVERT: M 70 ASP cc_start: 0.8327 (p0) cc_final: 0.7705 (t70) REVERT: N 34 ASN cc_start: 0.8355 (m110) cc_final: 0.7991 (m-40) REVERT: N 36 TYR cc_start: 0.7598 (m-80) cc_final: 0.6445 (m-80) REVERT: N 46 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5137 (tt) REVERT: N 62 PHE cc_start: 0.6424 (m-80) cc_final: 0.6179 (m-80) REVERT: N 86 TYR cc_start: 0.6899 (m-10) cc_final: 0.6687 (m-10) outliers start: 88 outliers final: 49 residues processed: 379 average time/residue: 0.5271 time to fit residues: 328.6439 Evaluate side-chains 356 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 299 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 103 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9087 > 50: distance: 27 - 32: 3.674 distance: 32 - 33: 5.364 distance: 33 - 34: 3.488 distance: 33 - 36: 7.064 distance: 34 - 35: 10.869 distance: 34 - 38: 7.364 distance: 36 - 37: 11.756 distance: 38 - 39: 19.981 distance: 39 - 40: 10.239 distance: 39 - 42: 32.646 distance: 40 - 41: 32.172 distance: 40 - 45: 6.583 distance: 42 - 43: 25.009 distance: 42 - 44: 20.705 distance: 45 - 46: 25.841 distance: 46 - 47: 32.924 distance: 46 - 49: 13.412 distance: 47 - 48: 30.507 distance: 47 - 54: 12.087 distance: 49 - 50: 12.840 distance: 50 - 51: 37.085 distance: 51 - 52: 11.832 distance: 51 - 53: 16.623 distance: 54 - 55: 12.699 distance: 55 - 56: 19.465 distance: 55 - 58: 17.444 distance: 56 - 57: 20.713 distance: 56 - 62: 23.312 distance: 58 - 59: 24.126 distance: 58 - 60: 14.183 distance: 59 - 61: 20.767 distance: 62 - 63: 8.053 distance: 63 - 64: 3.163 distance: 63 - 66: 16.860 distance: 64 - 65: 17.250 distance: 66 - 67: 12.376 distance: 67 - 68: 19.470 distance: 67 - 69: 23.768 distance: 68 - 70: 15.170 distance: 69 - 71: 22.873 distance: 70 - 72: 26.242 distance: 71 - 72: 25.619 distance: 72 - 73: 9.962 distance: 74 - 75: 6.843 distance: 75 - 76: 10.757 distance: 75 - 78: 4.729 distance: 76 - 77: 9.781 distance: 76 - 83: 13.754 distance: 79 - 80: 12.636 distance: 80 - 81: 7.892 distance: 80 - 82: 3.277 distance: 84 - 85: 9.887 distance: 84 - 87: 11.812 distance: 85 - 86: 18.064 distance: 85 - 88: 19.127 distance: 88 - 89: 18.414 distance: 89 - 90: 13.363 distance: 90 - 91: 15.728 distance: 90 - 92: 13.552 distance: 92 - 93: 13.871 distance: 93 - 94: 12.350 distance: 93 - 96: 11.458 distance: 94 - 95: 6.331 distance: 94 - 100: 12.127 distance: 96 - 97: 14.846 distance: 100 - 101: 32.214 distance: 101 - 102: 14.780 distance: 101 - 104: 9.622 distance: 102 - 103: 10.811 distance: 102 - 109: 13.342 distance: 104 - 105: 15.204 distance: 105 - 106: 21.803 distance: 106 - 107: 16.950 distance: 107 - 108: 15.096