Starting phenix.real_space_refine on Mon Aug 25 20:11:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtq_34263/08_2025/8gtq_34263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtq_34263/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gtq_34263/08_2025/8gtq_34263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtq_34263/08_2025/8gtq_34263.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gtq_34263/08_2025/8gtq_34263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtq_34263/08_2025/8gtq_34263.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.27, per 1000 atoms: 0.24 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.54 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: 7.36 Time building geometry restraints manager: 3.88 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: 0.02 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.370 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.310 ------------------------------------------------------------------------------- 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 : 14.32 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.05 (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 ARG 0.004 0.000 ARG C 102 TYR 0.024 0.002 TYR B 453 PHE 0.025 0.002 PHE B 86 TRP 0.015 0.002 TRP A 436 HIS 0.009 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00945 (31230) covalent geometry : angle 1.04834 (42456) SS BOND : bond 0.11200 ( 42) SS BOND : angle 8.72364 ( 84) hydrogen bonds : bond 0.20537 ( 1046) hydrogen bonds : angle 7.85653 ( 2940) link_BETA1-4 : bond 0.06542 ( 27) link_BETA1-4 : angle 5.60244 ( 81) link_NAG-ASN : bond 0.02959 ( 48) link_NAG-ASN : angle 9.24287 ( 144) *********************** 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 : 0.906 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: 0.7570 (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: 0.5904 (m-10) outliers start: 100 outliers final: 41 residues processed: 759 average time/residue: 0.2188 time to fit residues: 260.7981 Evaluate side-chains 385 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.0570 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.4860 ------------------------------------------------------------------------------- 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 422 ASN A 450 ASN A 607 GLN 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 173 GLN C 422 ASN C 450 ASN C 607 GLN C 613 GLN C 925 ASN 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 79 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.190015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122967 restraints weight = 49434.736| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.62 r_work: 0.3522 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 31347 Z= 0.150 Angle : 0.752 15.700 42765 Z= 0.377 Chirality : 0.048 0.384 4941 Planarity : 0.006 0.117 5388 Dihedral : 7.727 64.966 5709 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.71 % Favored : 93.96 % Rotamer: Outliers : 2.91 % Allowed : 13.24 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.13), residues: 3693 helix: 0.49 (0.20), residues: 641 sheet: -1.13 (0.15), residues: 1059 loop : -2.22 (0.12), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 995 TYR 0.019 0.001 TYR A 170 PHE 0.029 0.001 PHE B 823 TRP 0.019 0.001 TRP N 3 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00327 (31230) covalent geometry : angle 0.70804 (42456) SS BOND : bond 0.00486 ( 42) SS BOND : angle 2.95056 ( 84) hydrogen bonds : bond 0.05214 ( 1046) hydrogen bonds : angle 5.77271 ( 2940) link_BETA1-4 : bond 0.00978 ( 27) link_BETA1-4 : angle 2.94243 ( 81) link_NAG-ASN : bond 0.00510 ( 48) link_NAG-ASN : angle 3.22382 ( 144) *********************** 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 496 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 401 time to evaluate : 0.941 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: 0.8207 (p90) cc_final: 0.7880 (p90) REVERT: A 233 ILE cc_start: 0.5918 (mm) cc_final: 0.5224 (pt) REVERT: A 328 ARG cc_start: 0.6988 (mmt90) cc_final: 0.6714 (ttm-80) REVERT: A 740 MET cc_start: 0.8331 (ttm) cc_final: 0.7965 (mtp) REVERT: A 869 MET cc_start: 0.8004 (mtt) cc_final: 0.7736 (mtt) REVERT: A 950 ASP cc_start: 0.7753 (m-30) cc_final: 0.7420 (p0) REVERT: B 287 ASP cc_start: 0.7891 (t70) cc_final: 0.7584 (t70) REVERT: B 321 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7155 (mm-40) REVERT: B 613 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7840 (mm-40) REVERT: B 697 MET cc_start: 0.7856 (ptm) cc_final: 0.7612 (ptt) REVERT: B 759 PHE cc_start: 0.7447 (m-10) cc_final: 0.7195 (m-10) REVERT: B 779 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8039 (tp40) REVERT: B 790 LYS cc_start: 0.9071 (mttt) cc_final: 0.8764 (mttm) REVERT: B 854 LYS cc_start: 0.6494 (OUTLIER) cc_final: 0.5618 (UNCLASSIFIED) REVERT: C 314 GLN cc_start: 0.8494 (tt0) cc_final: 0.8213 (tm-30) REVERT: C 613 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: C 725 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: C 775 ASP cc_start: 0.7825 (m-30) cc_final: 0.7504 (m-30) REVERT: C 902 MET cc_start: 0.8607 (mmm) cc_final: 0.8235 (tpt) REVERT: C 969 LYS cc_start: 0.8382 (ptmm) cc_final: 0.7736 (tmmt) REVERT: C 984 LEU cc_start: 0.7818 (tp) cc_final: 0.6727 (tp) REVERT: L 89 GLN cc_start: 0.7734 (tt0) cc_final: 0.7297 (pt0) REVERT: I 34 MET cc_start: 0.7962 (mmm) cc_final: 0.7728 (mmm) REVERT: I 93 VAL cc_start: 0.6018 (t) cc_final: 0.5799 (p) REVERT: I 101 ASP cc_start: 0.7643 (t70) cc_final: 0.7395 (t0) REVERT: M 33 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8538 (tp) REVERT: M 70 ASP cc_start: 0.8132 (p0) cc_final: 0.7620 (t70) REVERT: M 71 PHE cc_start: 0.7670 (m-10) cc_final: 0.7388 (m-10) REVERT: N 34 ASN cc_start: 0.8568 (m110) cc_final: 0.8220 (m-40) REVERT: N 36 TYR cc_start: 0.7719 (m-80) cc_final: 0.6713 (m-80) REVERT: N 46 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4667 (tt) REVERT: N 50 ASP cc_start: 0.6810 (p0) cc_final: 0.6497 (p0) REVERT: N 62 PHE cc_start: 0.6916 (m-80) cc_final: 0.6702 (m-80) REVERT: N 87 TYR cc_start: 0.7623 (m-80) cc_final: 0.7339 (m-80) outliers start: 95 outliers final: 37 residues processed: 476 average time/residue: 0.1718 time to fit residues: 133.0200 Evaluate side-chains 372 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 327 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 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 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 588 THR 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 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain M residue 33 LEU 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 116 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 362 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 310 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN C 925 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN J 57 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.177226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105636 restraints weight = 48193.709| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.44 r_work: 0.3253 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 31347 Z= 0.335 Angle : 0.848 14.322 42765 Z= 0.422 Chirality : 0.053 0.320 4941 Planarity : 0.006 0.090 5388 Dihedral : 6.890 56.591 5657 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.90 % Favored : 92.88 % Rotamer: Outliers : 3.46 % Allowed : 14.43 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.13), residues: 3693 helix: 0.23 (0.20), residues: 660 sheet: -0.98 (0.15), residues: 1047 loop : -2.04 (0.12), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 995 TYR 0.023 0.002 TYR C 873 PHE 0.032 0.002 PHE A1103 TRP 0.016 0.002 TRP B1102 HIS 0.014 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00810 (31230) covalent geometry : angle 0.80589 (42456) SS BOND : bond 0.00736 ( 42) SS BOND : angle 3.15435 ( 84) hydrogen bonds : bond 0.05410 ( 1046) hydrogen bonds : angle 5.70020 ( 2940) link_BETA1-4 : bond 0.00758 ( 27) link_BETA1-4 : angle 2.77934 ( 81) link_NAG-ASN : bond 0.00668 ( 48) link_NAG-ASN : angle 3.45385 ( 144) *********************** 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 461 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 348 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8144 (p90) cc_final: 0.7860 (p90) REVERT: A 233 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.5674 (pt) REVERT: A 332 ILE cc_start: 0.4959 (OUTLIER) cc_final: 0.4706 (mt) REVERT: A 558 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8410 (mmmt) REVERT: A 574 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7111 (p0) REVERT: A 586 ASP cc_start: 0.7502 (m-30) cc_final: 0.6991 (m-30) REVERT: A 725 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: A 737 ASP cc_start: 0.7524 (t0) cc_final: 0.7146 (t70) REVERT: A 950 ASP cc_start: 0.8000 (m-30) cc_final: 0.7597 (p0) REVERT: A 984 LEU cc_start: 0.6763 (tp) cc_final: 0.6494 (tp) REVERT: B 321 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7595 (mm-40) REVERT: B 613 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8263 (mm-40) REVERT: B 697 MET cc_start: 0.8391 (ptm) cc_final: 0.8081 (ptt) REVERT: B 759 PHE cc_start: 0.7663 (m-80) cc_final: 0.6960 (m-10) REVERT: B 961 THR cc_start: 0.8222 (t) cc_final: 0.7989 (p) REVERT: B 1041 ASP cc_start: 0.8133 (m-30) cc_final: 0.7639 (t0) REVERT: C 115 GLN cc_start: 0.5983 (mm110) cc_final: 0.5544 (mm-40) REVERT: C 495 TYR cc_start: 0.1868 (OUTLIER) cc_final: 0.1525 (m-80) REVERT: C 541 PHE cc_start: 0.6030 (p90) cc_final: 0.5654 (p90) REVERT: C 558 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8097 (mmtt) REVERT: C 725 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: C 869 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7751 (mtp) REVERT: C 904 TYR cc_start: 0.7199 (m-10) cc_final: 0.6587 (m-10) REVERT: C 969 LYS cc_start: 0.8423 (ptmm) cc_final: 0.8112 (ttpt) REVERT: C 1001 LEU cc_start: 0.7452 (tp) cc_final: 0.7195 (tt) REVERT: C 1050 MET cc_start: 0.8668 (ptm) cc_final: 0.8413 (ptm) REVERT: L 31 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.5879 (p90) REVERT: L 46 LEU cc_start: 0.6276 (tt) cc_final: 0.6006 (tt) REVERT: L 55 GLU cc_start: 0.6655 (pt0) cc_final: 0.6398 (pt0) REVERT: L 61 ARG cc_start: 0.7110 (mtm180) cc_final: 0.6679 (mtm180) REVERT: I 87 ARG cc_start: 0.5404 (ptp-170) cc_final: 0.4881 (ptp-170) REVERT: I 101 ASP cc_start: 0.7937 (t70) cc_final: 0.7544 (t0) REVERT: I 114 GLN cc_start: 0.7921 (mm110) cc_final: 0.7204 (mt0) REVERT: M 32 TYR cc_start: 0.7976 (m-80) cc_final: 0.7603 (m-80) REVERT: M 70 ASP cc_start: 0.8362 (p0) cc_final: 0.7722 (t70) REVERT: J 91 THR cc_start: 0.7308 (OUTLIER) cc_final: 0.7055 (t) REVERT: N 34 ASN cc_start: 0.8749 (m110) cc_final: 0.8521 (m-40) REVERT: N 46 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5394 (tt) REVERT: N 62 PHE cc_start: 0.6626 (m-80) cc_final: 0.6382 (m-80) outliers start: 113 outliers final: 60 residues processed: 432 average time/residue: 0.1726 time to fit residues: 121.7618 Evaluate side-chains 376 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 304 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 80 ASP 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 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 952 VAL 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 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE 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 539 VAL Chi-restraints excluded: chain B residue 572 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 859 THR Chi-restraints excluded: chain B residue 1086 LYS 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 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 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 929 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain M residue 24 GLN 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 323 optimal weight: 20.0000 chunk 363 optimal weight: 30.0000 chunk 287 optimal weight: 1.9990 chunk 369 optimal weight: 20.0000 chunk 314 optimal weight: 10.0000 chunk 156 optimal weight: 0.0170 chunk 97 optimal weight: 0.8980 chunk 134 optimal weight: 0.0970 chunk 239 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 907 ASN A1135 ASN B 121 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN H 3 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN M 38 GLN M 79 GLN J 57 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.188407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117804 restraints weight = 48143.940| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.48 r_work: 0.3318 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31347 Z= 0.129 Angle : 0.659 11.558 42765 Z= 0.327 Chirality : 0.046 0.266 4941 Planarity : 0.004 0.051 5388 Dihedral : 6.057 59.000 5642 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.33 % Favored : 94.53 % Rotamer: Outliers : 2.76 % Allowed : 15.69 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.13), residues: 3693 helix: 0.78 (0.20), residues: 654 sheet: -0.66 (0.16), residues: 1027 loop : -1.75 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 38 TYR 0.011 0.001 TYR M 86 PHE 0.023 0.001 PHE C 541 TRP 0.015 0.001 TRP J 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00291 (31230) covalent geometry : angle 0.62299 (42456) SS BOND : bond 0.00546 ( 42) SS BOND : angle 2.57503 ( 84) hydrogen bonds : bond 0.03985 ( 1046) hydrogen bonds : angle 5.18649 ( 2940) link_BETA1-4 : bond 0.00814 ( 27) link_BETA1-4 : angle 2.53402 ( 81) link_NAG-ASN : bond 0.00427 ( 48) link_NAG-ASN : angle 2.64311 ( 144) *********************** 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 410 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 320 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8109 (p90) cc_final: 0.7840 (p90) REVERT: A 160 TYR cc_start: 0.7162 (p90) cc_final: 0.6594 (p90) REVERT: A 233 ILE cc_start: 0.6382 (mm) cc_final: 0.5901 (pt) REVERT: A 332 ILE cc_start: 0.4952 (OUTLIER) cc_final: 0.4654 (mt) REVERT: A 558 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8437 (mmmt) REVERT: A 586 ASP cc_start: 0.7469 (m-30) cc_final: 0.7000 (m-30) REVERT: A 725 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8593 (tt0) REVERT: A 737 ASP cc_start: 0.7622 (t0) cc_final: 0.7197 (t70) REVERT: A 869 MET cc_start: 0.8129 (mtt) cc_final: 0.7878 (mtt) REVERT: A 950 ASP cc_start: 0.7922 (m-30) cc_final: 0.7555 (p0) REVERT: B 153 MET cc_start: 0.3385 (ptm) cc_final: 0.2964 (tmm) REVERT: B 321 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7699 (mm-40) REVERT: B 613 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8321 (mm-40) REVERT: B 697 MET cc_start: 0.8374 (ptm) cc_final: 0.7990 (ptt) REVERT: B 725 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7043 (mt-10) REVERT: B 759 PHE cc_start: 0.7413 (m-80) cc_final: 0.6698 (m-10) REVERT: C 115 GLN cc_start: 0.5847 (mm110) cc_final: 0.5319 (mm110) REVERT: C 495 TYR cc_start: 0.1847 (OUTLIER) cc_final: 0.1520 (m-80) REVERT: C 558 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8104 (mmtt) REVERT: C 725 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: C 786 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8136 (mmmt) REVERT: C 904 TYR cc_start: 0.7153 (m-10) cc_final: 0.6873 (m-10) REVERT: C 969 LYS cc_start: 0.8287 (ptmm) cc_final: 0.7915 (ttmt) REVERT: C 1001 LEU cc_start: 0.7403 (tp) cc_final: 0.7150 (tt) REVERT: C 1050 MET cc_start: 0.8543 (ptm) cc_final: 0.8302 (ptm) REVERT: H 20 LEU cc_start: 0.7148 (tp) cc_final: 0.6859 (tp) REVERT: H 83 MET cc_start: 0.7026 (ptp) cc_final: 0.6353 (mtm) REVERT: L 31 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6255 (p90) REVERT: L 46 LEU cc_start: 0.6143 (tt) cc_final: 0.5840 (tt) REVERT: L 55 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6180 (pt0) REVERT: L 61 ARG cc_start: 0.6885 (mtm180) cc_final: 0.6668 (mtm180) REVERT: L 93 ASN cc_start: 0.7697 (t0) cc_final: 0.7000 (p0) REVERT: I 87 ARG cc_start: 0.5507 (ptp-170) cc_final: 0.5033 (ptp-170) REVERT: I 93 VAL cc_start: 0.6423 (t) cc_final: 0.6158 (p) REVERT: I 114 GLN cc_start: 0.7911 (mm110) cc_final: 0.7157 (mp10) REVERT: M 4 MET cc_start: 0.5116 (pmm) cc_final: 0.4082 (ptp) REVERT: M 32 TYR cc_start: 0.7956 (m-80) cc_final: 0.7468 (m-80) REVERT: M 70 ASP cc_start: 0.8439 (p0) cc_final: 0.7736 (t70) REVERT: J 19 ARG cc_start: 0.6325 (ttm170) cc_final: 0.6062 (ttm170) REVERT: J 91 THR cc_start: 0.7215 (OUTLIER) cc_final: 0.6967 (t) REVERT: N 34 ASN cc_start: 0.8683 (m110) cc_final: 0.8438 (m-40) REVERT: N 46 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.5230 (tt) REVERT: N 62 PHE cc_start: 0.6566 (m-80) cc_final: 0.6294 (m-10) REVERT: N 92 ASP cc_start: 0.7689 (m-30) cc_final: 0.7479 (m-30) outliers start: 90 outliers final: 43 residues processed: 387 average time/residue: 0.1782 time to fit residues: 112.5653 Evaluate side-chains 351 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 208 THR Chi-restraints excluded: chain A residue 332 ILE 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 725 GLU 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 A residue 995 ARG Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 127 VAL 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 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1086 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 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 785 VAL Chi-restraints excluded: chain C residue 866 THR 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 55 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain M residue 22 THR 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 58 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 103 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 316 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 chunk 294 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 chunk 317 optimal weight: 8.9990 chunk 35 optimal weight: 0.0570 chunk 262 optimal weight: 0.0020 overall best weight: 0.6908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 774 GLN C 955 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN J 57 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.188842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118454 restraints weight = 48169.724| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.48 r_work: 0.3325 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31347 Z= 0.119 Angle : 0.630 10.692 42765 Z= 0.311 Chirality : 0.045 0.242 4941 Planarity : 0.004 0.051 5388 Dihedral : 5.607 59.516 5642 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.48 % Rotamer: Outliers : 2.45 % Allowed : 16.42 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.13), residues: 3693 helix: 1.03 (0.21), residues: 661 sheet: -0.53 (0.16), residues: 1038 loop : -1.54 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 38 TYR 0.010 0.001 TYR A 904 PHE 0.029 0.001 PHE C 541 TRP 0.011 0.001 TRP L 35 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00271 (31230) covalent geometry : angle 0.59694 (42456) SS BOND : bond 0.00395 ( 42) SS BOND : angle 2.41832 ( 84) hydrogen bonds : bond 0.03634 ( 1046) hydrogen bonds : angle 4.99829 ( 2940) link_BETA1-4 : bond 0.00800 ( 27) link_BETA1-4 : angle 2.42889 ( 81) link_NAG-ASN : bond 0.00351 ( 48) link_NAG-ASN : angle 2.44319 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 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 402 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 322 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8170 (p90) cc_final: 0.7915 (p90) REVERT: A 160 TYR cc_start: 0.7136 (p90) cc_final: 0.6603 (p90) REVERT: A 233 ILE cc_start: 0.6374 (mm) cc_final: 0.5934 (pt) REVERT: A 558 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8504 (mmmt) REVERT: A 586 ASP cc_start: 0.7538 (m-30) cc_final: 0.6805 (m-30) REVERT: A 613 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8597 (mt0) REVERT: A 737 ASP cc_start: 0.7754 (t0) cc_final: 0.7313 (t70) REVERT: A 869 MET cc_start: 0.8181 (mtt) cc_final: 0.7932 (mtt) REVERT: A 950 ASP cc_start: 0.7922 (m-30) cc_final: 0.7540 (p0) REVERT: B 33 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8424 (p) REVERT: B 321 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7723 (mm-40) REVERT: B 613 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8261 (mm-40) REVERT: B 697 MET cc_start: 0.8475 (ptm) cc_final: 0.8087 (ptt) REVERT: B 725 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 759 PHE cc_start: 0.7375 (m-80) cc_final: 0.6647 (m-10) REVERT: C 115 GLN cc_start: 0.5885 (mm110) cc_final: 0.5335 (mm-40) REVERT: C 143 VAL cc_start: 0.6890 (OUTLIER) cc_final: 0.6358 (p) REVERT: C 495 TYR cc_start: 0.1705 (OUTLIER) cc_final: 0.1395 (m-80) REVERT: C 558 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8253 (mmtm) REVERT: C 725 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: C 786 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8181 (mmmt) REVERT: C 900 MET cc_start: 0.8280 (ttm) cc_final: 0.7809 (mtp) REVERT: C 969 LYS cc_start: 0.8402 (ptmm) cc_final: 0.8095 (ttpt) REVERT: C 1050 MET cc_start: 0.8538 (ptm) cc_final: 0.8316 (ptm) REVERT: L 31 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6384 (p90) REVERT: L 46 LEU cc_start: 0.6232 (tt) cc_final: 0.5953 (tt) REVERT: L 50 ASP cc_start: 0.7437 (t70) cc_final: 0.7189 (t0) REVERT: L 55 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.5463 (pt0) REVERT: L 93 ASN cc_start: 0.7628 (t0) cc_final: 0.6951 (p0) REVERT: I 87 ARG cc_start: 0.5528 (ptp-170) cc_final: 0.5073 (ptp-170) REVERT: I 114 GLN cc_start: 0.7939 (mm110) cc_final: 0.7107 (mp10) REVERT: M 4 MET cc_start: 0.4937 (pmm) cc_final: 0.4435 (ptp) REVERT: M 32 TYR cc_start: 0.7853 (m-80) cc_final: 0.7446 (m-80) REVERT: M 70 ASP cc_start: 0.8443 (p0) cc_final: 0.7727 (t70) REVERT: M 71 PHE cc_start: 0.7218 (m-80) cc_final: 0.6810 (m-10) REVERT: J 65 LYS cc_start: 0.6645 (tppt) cc_final: 0.6319 (tppt) REVERT: J 76 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7499 (mmtp) REVERT: J 91 THR cc_start: 0.7253 (OUTLIER) cc_final: 0.7009 (t) REVERT: N 46 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5568 (tt) REVERT: N 62 PHE cc_start: 0.6392 (m-80) cc_final: 0.6163 (m-10) REVERT: N 92 ASP cc_start: 0.7668 (m-30) cc_final: 0.7439 (m-30) outliers start: 80 outliers final: 38 residues processed: 381 average time/residue: 0.1741 time to fit residues: 107.9615 Evaluate side-chains 342 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 293 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN 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 143 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 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 723 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 105 SER 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 103 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 321 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 281 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 121 ASN B 519 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.185985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114431 restraints weight = 47932.682| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.48 r_work: 0.3264 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31347 Z= 0.196 Angle : 0.684 11.766 42765 Z= 0.340 Chirality : 0.047 0.258 4941 Planarity : 0.004 0.052 5388 Dihedral : 5.663 55.490 5642 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.93 % Rotamer: Outliers : 2.67 % Allowed : 16.73 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.13), residues: 3693 helix: 0.97 (0.21), residues: 659 sheet: -0.55 (0.15), residues: 1075 loop : -1.51 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 646 TYR 0.014 0.001 TYR B 265 PHE 0.025 0.002 PHE C 541 TRP 0.019 0.001 TRP N 35 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00476 (31230) covalent geometry : angle 0.65255 (42456) SS BOND : bond 0.00480 ( 42) SS BOND : angle 2.53532 ( 84) hydrogen bonds : bond 0.04279 ( 1046) hydrogen bonds : angle 5.12280 ( 2940) link_BETA1-4 : bond 0.00758 ( 27) link_BETA1-4 : angle 2.38251 ( 81) link_NAG-ASN : bond 0.00356 ( 48) link_NAG-ASN : angle 2.57892 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 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 397 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 310 time to evaluate : 1.150 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: 0.8138 (p90) cc_final: 0.7870 (p90) REVERT: A 160 TYR cc_start: 0.7167 (p90) cc_final: 0.6612 (p90) REVERT: A 197 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6378 (tp) REVERT: A 233 ILE cc_start: 0.6417 (mm) cc_final: 0.6018 (pt) REVERT: A 558 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8550 (mmmt) REVERT: A 586 ASP cc_start: 0.7595 (m-30) cc_final: 0.6874 (m-30) REVERT: A 725 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: A 737 ASP cc_start: 0.7905 (t0) cc_final: 0.7362 (t70) REVERT: A 950 ASP cc_start: 0.7980 (m-30) cc_final: 0.7528 (p0) REVERT: A 990 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7374 (mm-30) REVERT: B 33 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 215 ASP cc_start: 0.7265 (m-30) cc_final: 0.5687 (t0) REVERT: B 221 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8882 (t) REVERT: B 321 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7646 (mm-40) REVERT: B 613 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8143 (mm-40) REVERT: B 697 MET cc_start: 0.8512 (ptm) cc_final: 0.8165 (ptt) REVERT: B 725 GLU cc_start: 0.7637 (mt-10) cc_final: 0.6909 (mt-10) REVERT: B 743 CYS cc_start: 0.6639 (OUTLIER) cc_final: 0.6145 (p) REVERT: B 759 PHE cc_start: 0.7380 (m-80) cc_final: 0.6743 (m-10) REVERT: B 1041 ASP cc_start: 0.8162 (m-30) cc_final: 0.7736 (t0) REVERT: C 115 GLN cc_start: 0.5941 (mm110) cc_final: 0.5324 (mm-40) REVERT: C 143 VAL cc_start: 0.6977 (OUTLIER) cc_final: 0.6469 (p) REVERT: C 495 TYR cc_start: 0.1980 (OUTLIER) cc_final: 0.1714 (m-80) REVERT: C 558 LYS cc_start: 0.8572 (mmtt) cc_final: 0.8259 (mmtm) REVERT: C 725 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: C 786 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8211 (mmmt) REVERT: C 900 MET cc_start: 0.8279 (ttm) cc_final: 0.7953 (mtp) REVERT: C 904 TYR cc_start: 0.7280 (m-10) cc_final: 0.6697 (m-10) REVERT: C 969 LYS cc_start: 0.8465 (ptmm) cc_final: 0.8144 (ttpt) REVERT: C 1050 MET cc_start: 0.8543 (ptm) cc_final: 0.8320 (ptm) REVERT: H 83 MET cc_start: 0.7113 (ptp) cc_final: 0.6451 (mtt) REVERT: L 31 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6240 (p90) REVERT: L 46 LEU cc_start: 0.6308 (tt) cc_final: 0.6016 (tt) REVERT: L 50 ASP cc_start: 0.7610 (t70) cc_final: 0.7377 (t0) REVERT: I 87 ARG cc_start: 0.5512 (ptp-170) cc_final: 0.5078 (ptp-170) REVERT: I 114 GLN cc_start: 0.8034 (mm110) cc_final: 0.7329 (mp10) REVERT: M 4 MET cc_start: 0.5493 (pmm) cc_final: 0.5078 (ptp) REVERT: M 32 TYR cc_start: 0.7919 (m-80) cc_final: 0.7535 (m-80) REVERT: M 70 ASP cc_start: 0.8392 (p0) cc_final: 0.7708 (t70) REVERT: J 91 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7122 (t) REVERT: N 62 PHE cc_start: 0.6506 (m-80) cc_final: 0.6227 (m-10) REVERT: N 92 ASP cc_start: 0.7806 (m-30) cc_final: 0.7549 (m-30) outliers start: 87 outliers final: 53 residues processed: 377 average time/residue: 0.1830 time to fit residues: 111.9024 Evaluate side-chains 352 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 287 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 725 GLU 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 A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 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 743 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE 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 723 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 105 SER 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 J residue 105 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain N residue 103 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 318 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 chunk 232 optimal weight: 30.0000 chunk 358 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 363 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 chunk 316 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN J 57 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.181192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108131 restraints weight = 46829.797| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.64 r_work: 0.3218 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 31347 Z= 0.326 Angle : 0.810 21.228 42765 Z= 0.398 Chirality : 0.051 0.314 4941 Planarity : 0.005 0.063 5388 Dihedral : 6.105 52.971 5639 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.15 % Favored : 92.72 % Rotamer: Outliers : 2.94 % Allowed : 16.94 % Favored : 80.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.13), residues: 3693 helix: 0.68 (0.21), residues: 645 sheet: -0.74 (0.15), residues: 1094 loop : -1.63 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 995 TYR 0.020 0.002 TYR A 279 PHE 0.030 0.002 PHE A 133 TRP 0.020 0.002 TRP B 886 HIS 0.011 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00796 (31230) covalent geometry : angle 0.77061 (42456) SS BOND : bond 0.00471 ( 42) SS BOND : angle 3.26834 ( 84) hydrogen bonds : bond 0.05107 ( 1046) hydrogen bonds : angle 5.45827 ( 2940) link_BETA1-4 : bond 0.00671 ( 27) link_BETA1-4 : angle 2.42028 ( 81) link_NAG-ASN : bond 0.00470 ( 48) link_NAG-ASN : angle 3.20758 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 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 404 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 308 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.8389 (mm) cc_final: 0.8012 (tp) REVERT: A 140 PHE cc_start: 0.8098 (p90) cc_final: 0.7841 (p90) REVERT: A 197 ILE cc_start: 0.6744 (OUTLIER) cc_final: 0.6435 (tp) REVERT: A 233 ILE cc_start: 0.6909 (mm) cc_final: 0.6294 (pt) REVERT: A 558 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8533 (mmmt) REVERT: A 586 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.6834 (m-30) REVERT: A 725 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: A 950 ASP cc_start: 0.7993 (m-30) cc_final: 0.7532 (p0) REVERT: A 985 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8086 (p0) REVERT: A 1038 LYS cc_start: 0.8367 (mttm) cc_final: 0.8117 (mtmt) REVERT: B 33 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 215 ASP cc_start: 0.7336 (m-30) cc_final: 0.5628 (t0) REVERT: B 321 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7660 (mm-40) REVERT: B 571 ASP cc_start: 0.7641 (t0) cc_final: 0.7381 (t0) REVERT: B 613 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8672 (mt0) REVERT: B 697 MET cc_start: 0.8591 (ptm) cc_final: 0.8290 (ptt) REVERT: B 759 PHE cc_start: 0.7463 (m-80) cc_final: 0.7073 (m-80) REVERT: B 1041 ASP cc_start: 0.8307 (m-30) cc_final: 0.7665 (t0) REVERT: C 115 GLN cc_start: 0.5935 (mm110) cc_final: 0.5388 (mm-40) REVERT: C 495 TYR cc_start: 0.1906 (OUTLIER) cc_final: 0.1668 (m-80) REVERT: C 725 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: C 786 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8273 (mmmt) REVERT: C 969 LYS cc_start: 0.8506 (ptmm) cc_final: 0.8167 (ttpt) REVERT: H 83 MET cc_start: 0.6964 (ptp) cc_final: 0.6427 (mtt) REVERT: L 31 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6648 (p90) REVERT: I 101 ASP cc_start: 0.7965 (t70) cc_final: 0.7418 (t0) REVERT: I 114 GLN cc_start: 0.8050 (mm110) cc_final: 0.7333 (mp10) REVERT: M 4 MET cc_start: 0.5451 (pmm) cc_final: 0.5041 (ptp) REVERT: M 32 TYR cc_start: 0.8114 (m-80) cc_final: 0.7611 (m-80) REVERT: M 70 ASP cc_start: 0.8395 (p0) cc_final: 0.7722 (t70) REVERT: J 91 THR cc_start: 0.7420 (OUTLIER) cc_final: 0.7190 (t) REVERT: J 100 LYS cc_start: 0.6006 (ttmt) cc_final: 0.5636 (ttmt) REVERT: N 62 PHE cc_start: 0.6886 (m-80) cc_final: 0.6520 (m-10) REVERT: N 73 PHE cc_start: 0.8020 (t80) cc_final: 0.7634 (t80) outliers start: 96 outliers final: 68 residues processed: 381 average time/residue: 0.2118 time to fit residues: 129.9638 Evaluate side-chains 369 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 290 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 90 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 572 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL 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 196 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 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 743 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR 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 929 SER Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 105 SER 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 J residue 105 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 103 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 39 optimal weight: 40.0000 chunk 283 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 285 optimal weight: 0.7980 chunk 242 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 176 optimal weight: 0.9990 chunk 321 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 907 ASN B 957 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.183834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112007 restraints weight = 46859.735| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.62 r_work: 0.3263 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31347 Z= 0.149 Angle : 0.661 11.606 42765 Z= 0.327 Chirality : 0.046 0.305 4941 Planarity : 0.004 0.049 5388 Dihedral : 5.674 51.725 5639 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.77 % Favored : 94.12 % Rotamer: Outliers : 2.39 % Allowed : 17.65 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.13), residues: 3693 helix: 1.04 (0.21), residues: 642 sheet: -0.61 (0.15), residues: 1083 loop : -1.48 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 38 TYR 0.012 0.001 TYR B 269 PHE 0.029 0.001 PHE C 541 TRP 0.024 0.001 TRP N 35 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00353 (31230) covalent geometry : angle 0.62755 (42456) SS BOND : bond 0.00482 ( 42) SS BOND : angle 2.54898 ( 84) hydrogen bonds : bond 0.04011 ( 1046) hydrogen bonds : angle 5.10682 ( 2940) link_BETA1-4 : bond 0.00743 ( 27) link_BETA1-4 : angle 2.30176 ( 81) link_NAG-ASN : bond 0.00340 ( 48) link_NAG-ASN : angle 2.62347 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 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 383 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 305 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.8397 (mm) cc_final: 0.8039 (tp) REVERT: A 140 PHE cc_start: 0.8152 (p90) cc_final: 0.7905 (p90) REVERT: A 160 TYR cc_start: 0.7136 (p90) cc_final: 0.6576 (p90) REVERT: A 197 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6420 (tp) REVERT: A 233 ILE cc_start: 0.6899 (mm) cc_final: 0.6332 (pt) REVERT: A 558 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8505 (mmmt) REVERT: A 586 ASP cc_start: 0.7592 (m-30) cc_final: 0.6817 (m-30) REVERT: A 725 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: A 869 MET cc_start: 0.8177 (mtt) cc_final: 0.7965 (mtt) REVERT: A 907 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8221 (m110) REVERT: A 950 ASP cc_start: 0.7950 (m-30) cc_final: 0.7512 (p0) REVERT: A 1038 LYS cc_start: 0.8389 (mttm) cc_final: 0.8117 (mtmt) REVERT: B 215 ASP cc_start: 0.7379 (m-30) cc_final: 0.5654 (t0) REVERT: B 571 ASP cc_start: 0.7656 (t0) cc_final: 0.7360 (t0) REVERT: B 613 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8666 (mt0) REVERT: B 697 MET cc_start: 0.8527 (ptm) cc_final: 0.8214 (ptt) REVERT: B 743 CYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6309 (p) REVERT: B 759 PHE cc_start: 0.7053 (m-80) cc_final: 0.6675 (m-10) REVERT: B 918 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 1041 ASP cc_start: 0.8280 (m-30) cc_final: 0.7665 (t0) REVERT: C 115 GLN cc_start: 0.6030 (mm110) cc_final: 0.5525 (mm-40) REVERT: C 495 TYR cc_start: 0.1770 (OUTLIER) cc_final: 0.1532 (m-80) REVERT: C 725 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: C 735 SER cc_start: 0.8630 (t) cc_final: 0.8418 (m) REVERT: C 900 MET cc_start: 0.8254 (ttm) cc_final: 0.7927 (mtp) REVERT: C 904 TYR cc_start: 0.7243 (m-10) cc_final: 0.6748 (m-10) REVERT: C 969 LYS cc_start: 0.8526 (ptmm) cc_final: 0.8102 (ttmt) REVERT: H 25 SER cc_start: 0.7646 (m) cc_final: 0.7415 (t) REVERT: H 83 MET cc_start: 0.7047 (ptp) cc_final: 0.6424 (mtt) REVERT: L 31 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.6566 (p90) REVERT: L 50 ASP cc_start: 0.7538 (t0) cc_final: 0.7235 (t0) REVERT: L 89 GLN cc_start: 0.7820 (tt0) cc_final: 0.7201 (pt0) REVERT: I 87 ARG cc_start: 0.5595 (ptp-170) cc_final: 0.5068 (ptp-170) REVERT: I 114 GLN cc_start: 0.8020 (mm110) cc_final: 0.7298 (mp10) REVERT: M 4 MET cc_start: 0.5459 (pmm) cc_final: 0.4882 (ptp) REVERT: M 32 TYR cc_start: 0.8018 (m-80) cc_final: 0.7512 (m-80) REVERT: M 70 ASP cc_start: 0.8488 (p0) cc_final: 0.7808 (t70) REVERT: M 71 PHE cc_start: 0.7041 (m-10) cc_final: 0.6802 (m-10) REVERT: J 6 GLU cc_start: 0.7417 (mp0) cc_final: 0.7142 (pm20) REVERT: J 91 THR cc_start: 0.7384 (OUTLIER) cc_final: 0.7159 (t) REVERT: N 35 TRP cc_start: 0.5548 (m100) cc_final: 0.5065 (m100) REVERT: N 62 PHE cc_start: 0.6857 (m-80) cc_final: 0.6464 (m-80) REVERT: N 73 PHE cc_start: 0.7888 (t80) cc_final: 0.7448 (t80) REVERT: N 87 TYR cc_start: 0.7235 (m-80) cc_final: 0.6932 (m-80) outliers start: 78 outliers final: 52 residues processed: 360 average time/residue: 0.2110 time to fit residues: 122.6632 Evaluate side-chains 350 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 289 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 725 GLU 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 A residue 952 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU 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 723 THR 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 929 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain M residue 22 THR 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 72 THR Chi-restraints excluded: chain N residue 103 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 104 optimal weight: 0.0970 chunk 364 optimal weight: 20.0000 chunk 262 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 258 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 274 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.184895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.113355 restraints weight = 46550.877| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.60 r_work: 0.3302 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31347 Z= 0.124 Angle : 0.632 10.114 42765 Z= 0.313 Chirality : 0.045 0.266 4941 Planarity : 0.004 0.048 5388 Dihedral : 5.294 51.184 5636 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.63 % Favored : 94.26 % Rotamer: Outliers : 2.05 % Allowed : 18.20 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3693 helix: 1.32 (0.21), residues: 635 sheet: -0.43 (0.15), residues: 1072 loop : -1.36 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.011 0.001 TYR A 279 PHE 0.035 0.001 PHE L 73 TRP 0.018 0.001 TRP N 35 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00287 (31230) covalent geometry : angle 0.60219 (42456) SS BOND : bond 0.00377 ( 42) SS BOND : angle 2.11218 ( 84) hydrogen bonds : bond 0.03702 ( 1046) hydrogen bonds : angle 4.96282 ( 2940) link_BETA1-4 : bond 0.00742 ( 27) link_BETA1-4 : angle 2.24634 ( 81) link_NAG-ASN : bond 0.00337 ( 48) link_NAG-ASN : angle 2.49298 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 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 372 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 305 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.8396 (mm) cc_final: 0.7977 (tp) REVERT: A 140 PHE cc_start: 0.8129 (p90) cc_final: 0.7880 (p90) REVERT: A 197 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6429 (tp) REVERT: A 233 ILE cc_start: 0.6979 (mm) cc_final: 0.6249 (pt) REVERT: A 542 ASN cc_start: 0.7713 (t0) cc_final: 0.7309 (t0) REVERT: A 558 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8474 (mmmt) REVERT: A 586 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: A 725 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: A 907 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.7988 (m110) REVERT: A 950 ASP cc_start: 0.7909 (m-30) cc_final: 0.7475 (p0) REVERT: A 1038 LYS cc_start: 0.8375 (mttm) cc_final: 0.8085 (mtmt) REVERT: A 1092 GLU cc_start: 0.8315 (tp30) cc_final: 0.7992 (tp30) REVERT: A 1111 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7940 (pp20) REVERT: B 215 ASP cc_start: 0.7367 (m-30) cc_final: 0.5666 (t0) REVERT: B 221 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8771 (t) REVERT: B 571 ASP cc_start: 0.7731 (t0) cc_final: 0.7402 (t0) REVERT: B 697 MET cc_start: 0.8542 (ptm) cc_final: 0.8207 (ptt) REVERT: B 759 PHE cc_start: 0.6853 (m-80) cc_final: 0.6565 (m-10) REVERT: B 957 GLN cc_start: 0.7853 (mp10) cc_final: 0.7535 (mp10) REVERT: B 1041 ASP cc_start: 0.8230 (m-30) cc_final: 0.7632 (t0) REVERT: C 115 GLN cc_start: 0.5947 (mm110) cc_final: 0.5375 (mm-40) REVERT: C 725 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: C 735 SER cc_start: 0.8618 (t) cc_final: 0.8415 (m) REVERT: C 904 TYR cc_start: 0.7091 (m-10) cc_final: 0.6793 (m-10) REVERT: C 969 LYS cc_start: 0.8464 (ptmm) cc_final: 0.8116 (ttpt) REVERT: H 25 SER cc_start: 0.7611 (m) cc_final: 0.7372 (t) REVERT: H 83 MET cc_start: 0.6951 (ptp) cc_final: 0.6349 (mtt) REVERT: H 103 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7732 (ttm-80) REVERT: L 31 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.6611 (p90) REVERT: L 46 LEU cc_start: 0.6173 (tt) cc_final: 0.5966 (tt) REVERT: L 50 ASP cc_start: 0.7505 (t0) cc_final: 0.7292 (t0) REVERT: L 61 ARG cc_start: 0.7148 (mtm180) cc_final: 0.6817 (mtm180) REVERT: L 89 GLN cc_start: 0.7853 (tt0) cc_final: 0.7156 (pt0) REVERT: I 18 LEU cc_start: 0.5425 (mp) cc_final: 0.5101 (mt) REVERT: I 87 ARG cc_start: 0.5692 (ptp-170) cc_final: 0.5214 (ptp-170) REVERT: I 114 GLN cc_start: 0.7991 (mm110) cc_final: 0.7205 (mp10) REVERT: M 4 MET cc_start: 0.5533 (pmm) cc_final: 0.4922 (ptp) REVERT: M 32 TYR cc_start: 0.8150 (m-80) cc_final: 0.7878 (m-80) REVERT: M 70 ASP cc_start: 0.8528 (p0) cc_final: 0.7829 (t70) REVERT: M 71 PHE cc_start: 0.7046 (m-10) cc_final: 0.6831 (m-10) REVERT: J 91 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.7005 (t) REVERT: N 35 TRP cc_start: 0.5530 (m100) cc_final: 0.5226 (m100) REVERT: N 62 PHE cc_start: 0.6641 (m-80) cc_final: 0.6418 (m-80) REVERT: N 73 PHE cc_start: 0.7799 (t80) cc_final: 0.7529 (t80) outliers start: 67 outliers final: 47 residues processed: 352 average time/residue: 0.2119 time to fit residues: 120.3238 Evaluate side-chains 346 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 572 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 725 GLU 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 A residue 952 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU 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 723 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain M residue 22 THR 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 58 VAL Chi-restraints excluded: chain N residue 103 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 344 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 319 optimal weight: 30.0000 chunk 342 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 197 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.185390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113792 restraints weight = 46201.899| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.61 r_work: 0.3308 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31347 Z= 0.120 Angle : 0.628 10.735 42765 Z= 0.309 Chirality : 0.045 0.255 4941 Planarity : 0.004 0.049 5388 Dihedral : 5.091 50.926 5633 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 1.84 % Allowed : 18.47 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.14), residues: 3693 helix: 1.47 (0.21), residues: 636 sheet: -0.30 (0.16), residues: 1064 loop : -1.31 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.017 0.001 TYR B 741 PHE 0.030 0.001 PHE L 73 TRP 0.020 0.001 TRP N 35 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00278 (31230) covalent geometry : angle 0.59726 (42456) SS BOND : bond 0.00335 ( 42) SS BOND : angle 2.17799 ( 84) hydrogen bonds : bond 0.03523 ( 1046) hydrogen bonds : angle 4.89294 ( 2940) link_BETA1-4 : bond 0.00742 ( 27) link_BETA1-4 : angle 2.19246 ( 81) link_NAG-ASN : bond 0.00368 ( 48) link_NAG-ASN : angle 2.51144 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 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 359 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 299 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.8328 (mm) cc_final: 0.7968 (tp) REVERT: A 140 PHE cc_start: 0.8113 (p90) cc_final: 0.7868 (p90) REVERT: A 197 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6417 (tp) REVERT: A 233 ILE cc_start: 0.7000 (mm) cc_final: 0.6294 (pt) REVERT: A 329 PHE cc_start: 0.7344 (m-10) cc_final: 0.7036 (m-10) REVERT: A 542 ASN cc_start: 0.7731 (t0) cc_final: 0.7290 (t0) REVERT: A 558 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8452 (mmmt) REVERT: A 586 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: A 725 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8558 (tt0) REVERT: A 869 MET cc_start: 0.8112 (mtt) cc_final: 0.7896 (mtt) REVERT: A 950 ASP cc_start: 0.7897 (m-30) cc_final: 0.7460 (p0) REVERT: A 1111 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7910 (pp20) REVERT: B 215 ASP cc_start: 0.7362 (m-30) cc_final: 0.5704 (t0) REVERT: B 697 MET cc_start: 0.8535 (ptm) cc_final: 0.8202 (ptt) REVERT: B 759 PHE cc_start: 0.6863 (m-80) cc_final: 0.6618 (m-10) REVERT: B 1041 ASP cc_start: 0.8186 (m-30) cc_final: 0.7646 (t0) REVERT: C 115 GLN cc_start: 0.5916 (mm110) cc_final: 0.5341 (mm-40) REVERT: C 725 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: C 735 SER cc_start: 0.8614 (t) cc_final: 0.8410 (m) REVERT: C 904 TYR cc_start: 0.7126 (m-10) cc_final: 0.6894 (m-10) REVERT: C 969 LYS cc_start: 0.8474 (ptmm) cc_final: 0.8060 (ptmm) REVERT: H 25 SER cc_start: 0.7572 (m) cc_final: 0.7345 (t) REVERT: H 46 GLU cc_start: 0.7162 (tt0) cc_final: 0.6927 (tt0) REVERT: H 83 MET cc_start: 0.6894 (ptp) cc_final: 0.6343 (mtt) REVERT: H 103 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7784 (ttm-80) REVERT: L 31 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6619 (p90) REVERT: L 50 ASP cc_start: 0.7422 (t0) cc_final: 0.7164 (t0) REVERT: L 61 ARG cc_start: 0.7227 (mtm180) cc_final: 0.6914 (mtm180) REVERT: L 89 GLN cc_start: 0.7846 (tt0) cc_final: 0.7254 (pt0) REVERT: L 103 LYS cc_start: 0.8450 (ttmm) cc_final: 0.7860 (tptt) REVERT: I 18 LEU cc_start: 0.5367 (mp) cc_final: 0.5038 (mt) REVERT: I 87 ARG cc_start: 0.5715 (ptp-170) cc_final: 0.5223 (ptp-170) REVERT: I 114 GLN cc_start: 0.8045 (mm110) cc_final: 0.7192 (mp10) REVERT: M 4 MET cc_start: 0.5561 (pmm) cc_final: 0.4933 (ptp) REVERT: M 32 TYR cc_start: 0.8176 (m-80) cc_final: 0.7920 (m-80) REVERT: M 70 ASP cc_start: 0.8551 (p0) cc_final: 0.7816 (t70) REVERT: M 71 PHE cc_start: 0.7052 (m-10) cc_final: 0.6808 (m-10) REVERT: J 76 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7393 (mmtp) REVERT: J 91 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.7137 (t) REVERT: N 62 PHE cc_start: 0.6841 (m-80) cc_final: 0.6565 (m-80) REVERT: N 73 PHE cc_start: 0.7764 (t80) cc_final: 0.7450 (t80) outliers start: 60 outliers final: 47 residues processed: 339 average time/residue: 0.2109 time to fit residues: 115.1365 Evaluate side-chains 340 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 286 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 572 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU 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 723 THR 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 929 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 24 GLN 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 J residue 105 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 103 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 265 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.184951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.113385 restraints weight = 46802.071| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.60 r_work: 0.3301 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 31347 Z= 0.217 Angle : 0.816 59.199 42765 Z= 0.452 Chirality : 0.047 0.397 4941 Planarity : 0.004 0.047 5388 Dihedral : 5.091 50.909 5633 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 1.87 % Allowed : 18.38 % Favored : 79.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.14), residues: 3693 helix: 1.43 (0.21), residues: 636 sheet: -0.30 (0.16), residues: 1064 loop : -1.31 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.018 0.001 TYR B 741 PHE 0.029 0.001 PHE L 73 TRP 0.017 0.001 TRP N 35 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00467 (31230) covalent geometry : angle 0.79414 (42456) SS BOND : bond 0.00340 ( 42) SS BOND : angle 2.11871 ( 84) hydrogen bonds : bond 0.03707 ( 1046) hydrogen bonds : angle 4.89324 ( 2940) link_BETA1-4 : bond 0.00749 ( 27) link_BETA1-4 : angle 2.19543 ( 81) link_NAG-ASN : bond 0.00400 ( 48) link_NAG-ASN : angle 2.51208 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10361.74 seconds wall clock time: 177 minutes 30.30 seconds (10650.30 seconds total)