Starting phenix.real_space_refine on Sun Jul 5 21:18:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gtq_34263/07_2026/8gtq_34263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtq_34263/07_2026/8gtq_34263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gtq_34263/07_2026/8gtq_34263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtq_34263/07_2026/8gtq_34263.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtq_34263/07_2026/8gtq_34263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtq_34263/07_2026/8gtq_34263.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gtq_34263/07_2026/8gtq_34263.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gtq_34263/07_2026/8gtq_34263.cif" } 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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 10 Time building chain proxies: 5.55, per 1000 atoms: 0.18 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: 2.48 Conformation dependent library (CDL) restraints added in 981.8 milliseconds 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: 1.06 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: 7.12 Time building geometry restraints manager: 3.32 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: 16272 17.93 - 35.86: 1285 35.86 - 53.79: 268 53.79 - 71.72: 71 71.72 - 89.65: 29 Dihedral angle restraints: 17925 sinusoidal: 7014 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 17922 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: 0.03 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: 2.000 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 25.790 Find NCS groups from input model: 0.770 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 14.019 89.655 10803 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 are 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/Z covalent geometry : bond 0.00945 / 0.52 (31230) covalent geometry : angle 1.04834 / 0.62 (42456) SS BOND : bond 0.11200 / 8.51 ( 42) SS BOND : angle 8.72364 / 5.93 ( 84) hydrogen bonds : bond 0.20537 / 13.32 ( 1046) hydrogen bonds : angle 7.85653 / 5.18 ( 2940) link_BETA1-4 : bond 0.06542 / 4.50 ( 27) link_BETA1-4 : angle 5.60244 / 4.17 ( 81) link_NAG-ASN : bond 0.02959 / 1.88 ( 48) link_NAG-ASN : angle 9.24287 / 5.59 ( 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 : 1.032 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: 0.1805 time to fit residues: 218.4718 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 : 0.990 ------------------------------------------------------------------------------- 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... A 121 ASN A 164 ASN A 173 GLN A 422 ASN A 450 ASN A 607 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 907 ASN B 87 ASN B 121 ASN B 164 ASN B 422 ASN B 450 ASN B 532 ASN B 607 GLN B 613 GLN B 690 GLN B 774 GLN C 81 ASN C 121 ASN C 164 ASN C 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 = 0.190043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.123000 restraints weight = 49441.304| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.62 r_work: 0.3520 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31347 Z= 0.147 Angle : 0.752 15.360 42765 Z= 0.377 Chirality : 0.048 0.343 4941 Planarity : 0.006 0.118 5388 Dihedral : 7.020 64.937 4134 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.66 % Favored : 94.02 % Rotamer: Outliers : 2.94 % Allowed : 13.20 % 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 are not related in a simple way. whole: -2.08 (0.13), residues: 3693 helix: 0.48 (0.20), residues: 641 sheet: -1.12 (0.15), residues: 1059 loop : -2.21 (0.12), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 995 TYR 0.020 0.001 TYR A 170 PHE 0.032 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/Z covalent geometry : bond 0.00314 / 0.15 (31230) covalent geometry : angle 0.71004 / 0.37 (42456) SS BOND : bond 0.00429 / 0.29 ( 42) SS BOND : angle 2.88481 / 1.82 ( 84) hydrogen bonds : bond 0.05155 / 3.31 ( 1046) hydrogen bonds : angle 5.76463 / 3.81 ( 2940) link_BETA1-4 : bond 0.00710 / 0.44 ( 27) link_BETA1-4 : angle 2.80830 / 1.97 ( 81) link_NAG-ASN : bond 0.00509 / 0.36 ( 48) link_NAG-ASN : angle 3.15952 / 2.14 ( 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 499 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 403 time to evaluate : 0.788 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: 0.8195 (p90) cc_final: 0.7868 (p90) REVERT: A 233 ILE cc_start: 0.5901 (mm) cc_final: 0.5205 (pt) REVERT: A 328 ARG cc_start: 0.6956 (mmt90) cc_final: 0.6685 (ttm-80) REVERT: A 740 MET cc_start: 0.8324 (ttm) cc_final: 0.7982 (mtp) REVERT: A 869 MET cc_start: 0.7985 (mtt) cc_final: 0.7699 (mtt) REVERT: A 950 ASP cc_start: 0.7740 (m-30) cc_final: 0.7403 (p0) REVERT: B 169 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7589 (tm-30) REVERT: B 287 ASP cc_start: 0.7882 (t70) cc_final: 0.7568 (t70) REVERT: B 321 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7143 (mm-40) REVERT: B 613 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7833 (mm-40) REVERT: B 697 MET cc_start: 0.7851 (ptm) cc_final: 0.7624 (ptt) REVERT: B 759 PHE cc_start: 0.7435 (m-10) cc_final: 0.7150 (m-10) REVERT: B 779 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8027 (tp40) REVERT: B 790 LYS cc_start: 0.9071 (mttt) cc_final: 0.8755 (mttm) REVERT: B 854 LYS cc_start: 0.6344 (OUTLIER) cc_final: 0.5489 (UNCLASSIFIED) REVERT: C 314 GLN cc_start: 0.8500 (tt0) cc_final: 0.8204 (tm-30) REVERT: C 495 TYR cc_start: 0.1766 (OUTLIER) cc_final: 0.1201 (m-80) REVERT: C 613 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: C 775 ASP cc_start: 0.7814 (m-30) cc_final: 0.7494 (m-30) REVERT: C 902 MET cc_start: 0.8603 (mmm) cc_final: 0.8227 (tpt) REVERT: C 969 LYS cc_start: 0.8381 (ptmm) cc_final: 0.7735 (tmmt) REVERT: C 984 LEU cc_start: 0.7891 (tp) cc_final: 0.6856 (tp) REVERT: L 54 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7452 (mtt) REVERT: L 87 TYR cc_start: 0.7649 (m-80) cc_final: 0.7423 (m-80) REVERT: L 89 GLN cc_start: 0.7738 (tt0) cc_final: 0.7296 (pt0) REVERT: I 34 MET cc_start: 0.7925 (mmm) cc_final: 0.7694 (mmm) REVERT: I 93 VAL cc_start: 0.6013 (t) cc_final: 0.5794 (p) REVERT: I 101 ASP cc_start: 0.7605 (t70) cc_final: 0.7356 (t0) REVERT: M 33 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8528 (tp) REVERT: M 70 ASP cc_start: 0.8239 (p0) cc_final: 0.7700 (t70) REVERT: M 71 PHE cc_start: 0.7691 (m-10) cc_final: 0.7420 (m-10) REVERT: N 34 ASN cc_start: 0.8576 (m110) cc_final: 0.7830 (m-40) REVERT: N 36 TYR cc_start: 0.7706 (m-80) cc_final: 0.6678 (m-80) REVERT: N 46 LEU cc_start: 0.5152 (OUTLIER) cc_final: 0.4619 (tt) REVERT: N 50 ASP cc_start: 0.6813 (p0) cc_final: 0.6491 (p0) REVERT: N 62 PHE cc_start: 0.6905 (m-80) cc_final: 0.6691 (m-80) REVERT: N 87 TYR cc_start: 0.7606 (m-80) cc_final: 0.7318 (m-80) outliers start: 96 outliers final: 36 residues processed: 479 average time/residue: 0.1671 time to fit residues: 130.3737 Evaluate side-chains 371 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 326 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 495 TYR 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 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 MET 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: 20.0000 chunk 335 optimal weight: 4.9990 chunk 362 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 0.0000 chunk 300 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 237 optimal weight: 20.0000 chunk 310 optimal weight: 8.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN C 925 ASN L 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN J 57 ASN N 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.184217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113977 restraints weight = 48644.500| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.58 r_work: 0.3395 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 31347 Z= 0.163 Angle : 0.698 13.666 42765 Z= 0.346 Chirality : 0.047 0.288 4941 Planarity : 0.005 0.087 5388 Dihedral : 5.661 53.296 4082 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.50 % Favored : 94.29 % Rotamer: Outliers : 2.76 % Allowed : 14.49 % Favored : 82.75 % 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 are not related in a simple way. whole: -1.57 (0.13), residues: 3693 helix: 0.91 (0.20), residues: 639 sheet: -0.87 (0.15), residues: 1054 loop : -1.84 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 38 TYR 0.014 0.001 TYR B 265 PHE 0.034 0.002 PHE B 823 TRP 0.012 0.001 TRP N 3 HIS 0.007 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (31230) covalent geometry : angle 0.66061 / 0.34 (42456) SS BOND : bond 0.00559 / 0.38 ( 42) SS BOND : angle 2.68031 / 1.64 ( 84) hydrogen bonds : bond 0.04319 / 2.74 ( 1046) hydrogen bonds : angle 5.34522 / 3.55 ( 2940) link_BETA1-4 : bond 0.00764 / 0.46 ( 27) link_BETA1-4 : angle 2.47589 / 1.71 ( 81) link_NAG-ASN : bond 0.00661 / 0.37 ( 48) link_NAG-ASN : angle 2.88812 / 1.95 ( 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 438 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 348 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8203 (p90) cc_final: 0.7910 (p90) REVERT: A 233 ILE cc_start: 0.6156 (OUTLIER) cc_final: 0.5549 (pt) REVERT: A 332 ILE cc_start: 0.5213 (OUTLIER) cc_final: 0.4909 (mt) REVERT: A 558 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8304 (mmmt) REVERT: A 725 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: A 950 ASP cc_start: 0.7882 (m-30) cc_final: 0.7507 (p0) REVERT: B 53 ASP cc_start: 0.7767 (t0) cc_final: 0.7563 (t0) REVERT: B 153 MET cc_start: 0.3939 (ptm) cc_final: 0.3557 (tmm) REVERT: B 221 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8917 (t) REVERT: B 321 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7594 (mm-40) REVERT: B 613 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8081 (mm-40) REVERT: B 697 MET cc_start: 0.8235 (ptm) cc_final: 0.7940 (ptt) REVERT: B 759 PHE cc_start: 0.7832 (m-80) cc_final: 0.7043 (m-10) REVERT: B 790 LYS cc_start: 0.9146 (mttt) cc_final: 0.8892 (mttm) REVERT: C 115 GLN cc_start: 0.5877 (mm110) cc_final: 0.5431 (mm-40) REVERT: C 314 GLN cc_start: 0.8651 (tt0) cc_final: 0.7907 (tm-30) REVERT: C 495 TYR cc_start: 0.1339 (OUTLIER) cc_final: 0.0943 (m-80) REVERT: C 558 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8181 (mmtm) REVERT: C 613 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8343 (mt0) REVERT: C 725 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: C 786 LYS cc_start: 0.8332 (mmmt) cc_final: 0.8051 (mmmt) REVERT: C 902 MET cc_start: 0.8639 (mmm) cc_final: 0.8195 (tpt) REVERT: C 904 TYR cc_start: 0.7203 (m-10) cc_final: 0.6938 (m-10) REVERT: C 969 LYS cc_start: 0.8289 (ptmm) cc_final: 0.8003 (ttmt) REVERT: C 1001 LEU cc_start: 0.7296 (tp) cc_final: 0.7095 (tt) REVERT: L 21 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7247 (tp) REVERT: L 55 GLU cc_start: 0.6859 (pt0) cc_final: 0.6477 (pt0) REVERT: L 87 TYR cc_start: 0.7637 (m-80) cc_final: 0.7319 (m-80) REVERT: L 89 GLN cc_start: 0.7689 (tt0) cc_final: 0.6994 (tm-30) REVERT: L 93 ASN cc_start: 0.7656 (t0) cc_final: 0.6966 (p0) REVERT: I 13 GLN cc_start: 0.8024 (mp10) cc_final: 0.7807 (mp10) REVERT: I 93 VAL cc_start: 0.6432 (t) cc_final: 0.6186 (p) REVERT: M 70 ASP cc_start: 0.8446 (p0) cc_final: 0.7774 (t70) REVERT: M 71 PHE cc_start: 0.7518 (m-10) cc_final: 0.7147 (m-10) REVERT: J 91 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.6965 (t) REVERT: N 34 ASN cc_start: 0.8717 (m110) cc_final: 0.8223 (m-40) REVERT: N 36 TYR cc_start: 0.7723 (m-80) cc_final: 0.6701 (m-80) REVERT: N 46 LEU cc_start: 0.5321 (OUTLIER) cc_final: 0.4750 (tt) REVERT: N 62 PHE cc_start: 0.6611 (m-80) cc_final: 0.6268 (m-80) outliers start: 90 outliers final: 39 residues processed: 421 average time/residue: 0.1731 time to fit residues: 120.6480 Evaluate side-chains 361 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 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 666 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 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 866 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 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 L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 69 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 323 optimal weight: 1.9990 chunk 363 optimal weight: 40.0000 chunk 287 optimal weight: 1.9990 chunk 369 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 239 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN B 121 ASN B 913 GLN H 3 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN J 57 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.189093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118635 restraints weight = 48270.886| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.50 r_work: 0.3332 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31347 Z= 0.162 Angle : 0.662 10.680 42765 Z= 0.329 Chirality : 0.046 0.275 4941 Planarity : 0.005 0.081 5388 Dihedral : 5.253 56.878 4070 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.61 % Favored : 94.26 % Rotamer: Outliers : 2.91 % Allowed : 15.07 % Favored : 82.02 % 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 are not related in a simple way. whole: -1.35 (0.13), residues: 3693 helix: 0.99 (0.21), residues: 655 sheet: -0.64 (0.16), residues: 993 loop : -1.71 (0.12), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 38 TYR 0.012 0.001 TYR B 269 PHE 0.023 0.001 PHE N 96 TRP 0.021 0.001 TRP J 47 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (31230) covalent geometry : angle 0.63102 / 0.32 (42456) SS BOND : bond 0.00339 / 0.23 ( 42) SS BOND : angle 2.43093 / 1.54 ( 84) hydrogen bonds : bond 0.04053 / 2.58 ( 1046) hydrogen bonds : angle 5.15516 / 3.42 ( 2940) link_BETA1-4 : bond 0.00794 / 0.46 ( 27) link_BETA1-4 : angle 2.30748 / 1.59 ( 81) link_NAG-ASN : bond 0.00352 / 0.22 ( 48) link_NAG-ASN : angle 2.49077 / 1.73 ( 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 418 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 323 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8133 (p90) cc_final: 0.7881 (p90) REVERT: A 233 ILE cc_start: 0.6328 (mm) cc_final: 0.5842 (pt) REVERT: A 558 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8406 (mmmt) REVERT: A 586 ASP cc_start: 0.7164 (m-30) cc_final: 0.6794 (m-30) REVERT: A 823 PHE cc_start: 0.7676 (m-80) cc_final: 0.7397 (m-80) REVERT: A 950 ASP cc_start: 0.7939 (m-30) cc_final: 0.7507 (p0) REVERT: B 153 MET cc_start: 0.3572 (ptm) cc_final: 0.3153 (tmm) REVERT: B 221 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8890 (t) REVERT: B 321 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7698 (mm-40) REVERT: B 613 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8177 (mm-40) REVERT: B 697 MET cc_start: 0.8331 (ptm) cc_final: 0.7953 (ptt) REVERT: B 759 PHE cc_start: 0.7100 (m-80) cc_final: 0.6516 (m-10) REVERT: B 790 LYS cc_start: 0.9170 (mttt) cc_final: 0.8794 (mttm) REVERT: C 115 GLN cc_start: 0.5829 (mm110) cc_final: 0.5207 (mm110) REVERT: C 237 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.5880 (mtm-85) REVERT: C 495 TYR cc_start: 0.1450 (OUTLIER) cc_final: 0.1093 (m-80) REVERT: C 558 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8226 (mmtm) REVERT: C 613 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8763 (mt0) REVERT: C 725 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: C 900 MET cc_start: 0.8270 (ttm) cc_final: 0.7978 (mtp) REVERT: C 904 TYR cc_start: 0.7161 (m-10) cc_final: 0.6915 (m-10) REVERT: C 969 LYS cc_start: 0.8277 (ptmm) cc_final: 0.8001 (ttpt) REVERT: C 1001 LEU cc_start: 0.7389 (tp) cc_final: 0.7162 (tt) REVERT: C 1050 MET cc_start: 0.8522 (ptm) cc_final: 0.8291 (ptm) REVERT: H 3 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7136 (mp10) REVERT: L 31 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6630 (p90) REVERT: L 87 TYR cc_start: 0.7699 (m-80) cc_final: 0.7327 (m-80) REVERT: I 13 GLN cc_start: 0.8077 (mp10) cc_final: 0.7846 (mp10) REVERT: I 18 LEU cc_start: 0.5395 (mp) cc_final: 0.5021 (mt) REVERT: I 93 VAL cc_start: 0.6478 (t) cc_final: 0.6238 (p) REVERT: I 114 GLN cc_start: 0.7924 (mm110) cc_final: 0.7136 (mp10) REVERT: M 4 MET cc_start: 0.4941 (pmm) cc_final: 0.4070 (ptp) REVERT: M 39 LYS cc_start: 0.7107 (mmtp) cc_final: 0.6070 (tmmt) REVERT: M 70 ASP cc_start: 0.8494 (p0) cc_final: 0.7742 (t70) REVERT: M 71 PHE cc_start: 0.7234 (m-10) cc_final: 0.7031 (m-10) REVERT: J 91 THR cc_start: 0.7224 (OUTLIER) cc_final: 0.6990 (t) REVERT: N 34 ASN cc_start: 0.8616 (m110) cc_final: 0.8175 (m-40) REVERT: N 36 TYR cc_start: 0.7561 (m-80) cc_final: 0.6611 (m-80) REVERT: N 62 PHE cc_start: 0.6612 (m-80) cc_final: 0.6303 (m-80) REVERT: N 86 TYR cc_start: 0.6851 (m-10) cc_final: 0.6605 (m-10) outliers start: 95 outliers final: 51 residues processed: 394 average time/residue: 0.1696 time to fit residues: 109.0711 Evaluate side-chains 357 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 296 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 382 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS 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 997 ILE 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 200 TYR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 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 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 224 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain J residue 46 GLU 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 72 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 103 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 316 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 177 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 294 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 317 optimal weight: 8.9990 chunk 35 optimal weight: 0.0570 chunk 262 optimal weight: 0.7980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 644 GLN C 955 ASN L 89 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN J 57 ASN J 98 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.189852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119924 restraints weight = 48286.225| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.49 r_work: 0.3348 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31347 Z= 0.115 Angle : 0.614 9.655 42765 Z= 0.304 Chirality : 0.045 0.220 4941 Planarity : 0.004 0.051 5388 Dihedral : 5.002 59.409 4070 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.36 % Favored : 94.50 % Rotamer: Outliers : 2.39 % Allowed : 15.93 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 3693 helix: 1.23 (0.21), residues: 658 sheet: -0.42 (0.16), residues: 1041 loop : -1.55 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 38 TYR 0.012 0.001 TYR C 655 PHE 0.024 0.001 PHE L 73 TRP 0.014 0.001 TRP N 35 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (31230) covalent geometry : angle 0.58523 / 0.30 (42456) SS BOND : bond 0.00450 / 0.33 ( 42) SS BOND : angle 2.20328 / 1.39 ( 84) hydrogen bonds : bond 0.03577 / 2.30 ( 1046) hydrogen bonds : angle 4.94830 / 3.27 ( 2940) link_BETA1-4 : bond 0.00738 / 0.43 ( 27) link_BETA1-4 : angle 2.23806 / 1.54 ( 81) link_NAG-ASN : bond 0.00319 / 0.21 ( 48) link_NAG-ASN : angle 2.27076 / 1.59 ( 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 395 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 317 time to evaluate : 0.919 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: 0.8089 (p90) cc_final: 0.7854 (p90) REVERT: A 233 ILE cc_start: 0.6319 (mm) cc_final: 0.5873 (pt) REVERT: A 558 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8453 (mmmt) REVERT: A 586 ASP cc_start: 0.7332 (m-30) cc_final: 0.6876 (m-30) REVERT: A 737 ASP cc_start: 0.7526 (t0) cc_final: 0.7100 (t70) REVERT: A 869 MET cc_start: 0.8141 (mtt) cc_final: 0.7834 (mtt) REVERT: A 950 ASP cc_start: 0.7903 (m-30) cc_final: 0.7514 (p0) REVERT: B 33 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8415 (p) REVERT: B 153 MET cc_start: 0.3462 (ptm) cc_final: 0.3082 (tmm) REVERT: B 321 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7679 (mm-40) REVERT: B 613 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8202 (mm-40) REVERT: B 697 MET cc_start: 0.8423 (ptm) cc_final: 0.7958 (ptt) REVERT: B 725 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6952 (mt-10) REVERT: B 759 PHE cc_start: 0.7261 (m-80) cc_final: 0.6670 (m-10) REVERT: B 790 LYS cc_start: 0.9183 (mttt) cc_final: 0.8813 (mttm) REVERT: C 52 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8464 (tm-30) REVERT: C 237 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5744 (mtm-85) REVERT: C 495 TYR cc_start: 0.1490 (OUTLIER) cc_final: 0.1270 (m-80) REVERT: C 558 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8243 (mmtm) REVERT: C 869 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7633 (mtp) REVERT: C 969 LYS cc_start: 0.8296 (ptmm) cc_final: 0.7592 (ttpp) REVERT: C 1001 LEU cc_start: 0.7344 (tp) cc_final: 0.7102 (tt) REVERT: C 1050 MET cc_start: 0.8518 (ptm) cc_final: 0.8248 (ptm) REVERT: H 3 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: L 87 TYR cc_start: 0.7654 (m-80) cc_final: 0.7272 (m-80) REVERT: L 89 GLN cc_start: 0.7565 (tt0) cc_final: 0.6381 (tm-30) REVERT: L 93 ASN cc_start: 0.7811 (t0) cc_final: 0.7277 (p0) REVERT: I 18 LEU cc_start: 0.5183 (mp) cc_final: 0.4860 (mt) REVERT: I 114 GLN cc_start: 0.7953 (mm110) cc_final: 0.7210 (mp10) REVERT: M 4 MET cc_start: 0.5287 (pmm) cc_final: 0.4202 (ptp) REVERT: M 39 LYS cc_start: 0.7220 (mmtp) cc_final: 0.6108 (tmmt) REVERT: M 70 ASP cc_start: 0.8561 (p0) cc_final: 0.7769 (t70) REVERT: J 65 LYS cc_start: 0.6650 (tppt) cc_final: 0.6233 (tppt) REVERT: J 76 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7456 (mmtp) REVERT: J 91 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.7083 (t) REVERT: N 36 TYR cc_start: 0.7558 (m-80) cc_final: 0.6689 (m-80) REVERT: N 46 LEU cc_start: 0.5547 (OUTLIER) cc_final: 0.5301 (tt) outliers start: 78 outliers final: 47 residues processed: 374 average time/residue: 0.1615 time to fit residues: 99.1956 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 : 1.068 ------------------------------------------------------------------------------- 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 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 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS 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 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 ASP 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 723 THR 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 237 ARG 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 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 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain I residue 69 THR 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 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 93 VAL 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 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: 1.9990 chunk 13 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 281 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.188572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118141 restraints weight = 48250.236| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.47 r_work: 0.3316 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 31347 Z= 0.143 Angle : 0.637 19.190 42765 Z= 0.315 Chirality : 0.047 0.812 4941 Planarity : 0.004 0.049 5388 Dihedral : 4.816 58.697 4067 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.55 % Favored : 94.34 % Rotamer: Outliers : 2.33 % Allowed : 16.45 % Favored : 81.22 % 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 are not related in a simple way. whole: -0.98 (0.13), residues: 3693 helix: 1.19 (0.21), residues: 665 sheet: -0.35 (0.16), residues: 1008 loop : -1.48 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 38 TYR 0.010 0.001 TYR B 269 PHE 0.023 0.001 PHE C 565 TRP 0.008 0.001 TRP M 35 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (31230) covalent geometry : angle 0.60352 / 0.31 (42456) SS BOND : bond 0.00503 / 0.36 ( 42) SS BOND : angle 2.07674 / 1.31 ( 84) hydrogen bonds : bond 0.03782 / 2.44 ( 1046) hydrogen bonds : angle 4.88667 / 3.24 ( 2940) link_BETA1-4 : bond 0.00720 / 0.43 ( 27) link_BETA1-4 : angle 2.18031 / 1.49 ( 81) link_NAG-ASN : bond 0.00375 / 0.22 ( 48) link_NAG-ASN : angle 2.82326 / 2.02 ( 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 385 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 309 time to evaluate : 1.110 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 197 ILE cc_start: 0.6516 (OUTLIER) cc_final: 0.6158 (tp) REVERT: A 233 ILE cc_start: 0.6342 (mm) cc_final: 0.5940 (pt) REVERT: A 558 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8545 (mmmt) REVERT: A 586 ASP cc_start: 0.7312 (m-30) cc_final: 0.6851 (m-30) REVERT: A 737 ASP cc_start: 0.7749 (t0) cc_final: 0.7306 (t70) REVERT: A 869 MET cc_start: 0.8197 (mtt) cc_final: 0.7878 (mtt) REVERT: A 950 ASP cc_start: 0.7935 (m-30) cc_final: 0.7516 (p0) REVERT: A 1111 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: A 1142 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8115 (mm-40) REVERT: B 33 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8422 (p) REVERT: B 321 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7698 (mm-40) REVERT: B 697 MET cc_start: 0.8525 (ptm) cc_final: 0.8058 (ptt) REVERT: B 725 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7048 (mt-10) REVERT: B 759 PHE cc_start: 0.7365 (m-80) cc_final: 0.6677 (m-10) REVERT: C 52 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8450 (tm-30) REVERT: C 558 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8235 (mmtm) REVERT: C 725 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: C 869 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7582 (mtp) REVERT: C 969 LYS cc_start: 0.8336 (ptmm) cc_final: 0.7648 (ttpp) REVERT: C 1050 MET cc_start: 0.8518 (ptm) cc_final: 0.8259 (ptm) REVERT: L 31 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6469 (p90) REVERT: L 87 TYR cc_start: 0.7666 (m-80) cc_final: 0.7262 (m-80) REVERT: L 93 ASN cc_start: 0.7677 (t0) cc_final: 0.7453 (t0) REVERT: I 18 LEU cc_start: 0.5322 (mp) cc_final: 0.5045 (mt) REVERT: I 73 ASP cc_start: 0.6812 (t0) cc_final: 0.6608 (t0) REVERT: I 114 GLN cc_start: 0.8045 (mm110) cc_final: 0.7355 (mp10) REVERT: M 4 MET cc_start: 0.4949 (pmm) cc_final: 0.4301 (ptp) REVERT: M 39 LYS cc_start: 0.7102 (mmtp) cc_final: 0.6156 (tmmt) REVERT: M 70 ASP cc_start: 0.8657 (p0) cc_final: 0.8046 (m-30) REVERT: J 76 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7493 (mmtp) REVERT: J 91 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.7234 (t) REVERT: J 100 LYS cc_start: 0.6541 (tppp) cc_final: 0.6290 (tptm) REVERT: N 87 TYR cc_start: 0.7127 (m-80) cc_final: 0.6828 (m-80) outliers start: 76 outliers final: 51 residues processed: 369 average time/residue: 0.1606 time to fit residues: 98.0928 Evaluate side-chains 347 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS 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 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 127 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 197 ILE 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 723 THR 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 224 GLU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain I residue 37 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 318 optimal weight: 8.9990 chunk 234 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 336 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 chunk 358 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 363 optimal weight: 30.0000 chunk 71 optimal weight: 0.1980 chunk 316 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 519 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN J 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.186769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115712 restraints weight = 48076.981| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.47 r_work: 0.3278 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31347 Z= 0.185 Angle : 0.677 15.001 42765 Z= 0.334 Chirality : 0.047 0.632 4941 Planarity : 0.004 0.049 5388 Dihedral : 4.780 56.741 4061 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.90 % Favored : 93.99 % Rotamer: Outliers : 2.57 % Allowed : 16.82 % Favored : 80.61 % 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 are not related in a simple way. whole: -0.95 (0.14), residues: 3693 helix: 1.12 (0.21), residues: 656 sheet: -0.36 (0.15), residues: 1087 loop : -1.42 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 38 TYR 0.029 0.001 TYR B 741 PHE 0.026 0.002 PHE C 565 TRP 0.019 0.001 TRP N 35 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (31230) covalent geometry : angle 0.64497 / 0.33 (42456) SS BOND : bond 0.00506 / 0.36 ( 42) SS BOND : angle 2.47734 / 1.51 ( 84) hydrogen bonds : bond 0.04115 / 2.63 ( 1046) hydrogen bonds : angle 5.00530 / 3.33 ( 2940) link_BETA1-4 : bond 0.00735 / 0.43 ( 27) link_BETA1-4 : angle 2.15435 / 1.48 ( 81) link_NAG-ASN : bond 0.00334 / 0.20 ( 48) link_NAG-ASN : angle 2.68636 / 1.87 ( 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 398 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 314 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8095 (p90) cc_final: 0.7562 (p90) REVERT: A 197 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6396 (tp) REVERT: A 233 ILE cc_start: 0.6433 (mm) cc_final: 0.6083 (pt) REVERT: A 558 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8573 (mmmt) REVERT: A 586 ASP cc_start: 0.7351 (m-30) cc_final: 0.6876 (m-30) REVERT: A 725 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: A 737 ASP cc_start: 0.7726 (t0) cc_final: 0.7298 (t70) REVERT: A 950 ASP cc_start: 0.7992 (m-30) cc_final: 0.7552 (p0) REVERT: B 33 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8480 (p) REVERT: B 142 ASP cc_start: 0.6260 (OUTLIER) cc_final: 0.6044 (m-30) REVERT: B 215 ASP cc_start: 0.7337 (m-30) cc_final: 0.5714 (t0) REVERT: B 221 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8905 (t) REVERT: B 321 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7654 (mm-40) REVERT: B 571 ASP cc_start: 0.7833 (t0) cc_final: 0.7539 (t0) REVERT: B 697 MET cc_start: 0.8563 (ptm) cc_final: 0.8130 (ptt) REVERT: B 725 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6991 (mt-10) REVERT: B 759 PHE cc_start: 0.7497 (m-80) cc_final: 0.6829 (m-10) REVERT: B 1041 ASP cc_start: 0.8197 (m-30) cc_final: 0.7720 (t0) REVERT: C 558 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8279 (mmtm) REVERT: C 725 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: C 869 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7472 (mtp) REVERT: C 904 TYR cc_start: 0.7212 (m-10) cc_final: 0.6905 (m-10) REVERT: C 969 LYS cc_start: 0.8413 (ptmm) cc_final: 0.7595 (tmmt) REVERT: C 1050 MET cc_start: 0.8542 (ptm) cc_final: 0.8311 (ptm) REVERT: H 83 MET cc_start: 0.7376 (ptp) cc_final: 0.6612 (mtm) REVERT: L 31 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6523 (p90) REVERT: L 87 TYR cc_start: 0.7773 (m-80) cc_final: 0.7363 (m-80) REVERT: L 93 ASN cc_start: 0.7730 (t0) cc_final: 0.7473 (t0) REVERT: I 114 GLN cc_start: 0.8049 (mm110) cc_final: 0.7356 (mp10) REVERT: M 4 MET cc_start: 0.5537 (pmm) cc_final: 0.4466 (ptp) REVERT: M 39 LYS cc_start: 0.7107 (mmtp) cc_final: 0.6150 (tmmt) REVERT: M 70 ASP cc_start: 0.8533 (p0) cc_final: 0.7981 (m-30) REVERT: J 65 LYS cc_start: 0.6591 (tppt) cc_final: 0.6335 (tppt) REVERT: J 91 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.7122 (t) REVERT: N 24 GLN cc_start: 0.7398 (mp10) cc_final: 0.7156 (mp10) REVERT: N 87 TYR cc_start: 0.7155 (m-80) cc_final: 0.6642 (m-80) outliers start: 84 outliers final: 55 residues processed: 376 average time/residue: 0.1718 time to fit residues: 106.0719 Evaluate side-chains 355 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 290 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 649 CYS 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 1117 THR 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 127 VAL 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 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 641 ASN Chi-restraints excluded: chain B residue 723 THR 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 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 224 GLU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 ASP 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 46 GLU 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 74 THR Chi-restraints excluded: chain N residue 88 CYS 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: 20.0000 chunk 283 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 285 optimal weight: 3.9990 chunk 242 optimal weight: 0.4980 chunk 237 optimal weight: 20.0000 chunk 176 optimal weight: 0.1980 chunk 321 optimal weight: 9.9990 chunk 280 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.188995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118760 restraints weight = 48347.785| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.48 r_work: 0.3324 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 31347 Z= 0.109 Angle : 0.604 14.124 42765 Z= 0.299 Chirality : 0.045 0.534 4941 Planarity : 0.004 0.049 5388 Dihedral : 4.549 55.953 4061 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.56 % Rotamer: Outliers : 1.69 % Allowed : 17.46 % Favored : 80.85 % 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 are not related in a simple way. whole: -0.71 (0.14), residues: 3693 helix: 1.33 (0.21), residues: 661 sheet: -0.22 (0.16), residues: 1083 loop : -1.27 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 38 TYR 0.010 0.001 TYR B 741 PHE 0.034 0.001 PHE L 73 TRP 0.014 0.001 TRP M 35 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (31230) covalent geometry : angle 0.57581 / 0.29 (42456) SS BOND : bond 0.00345 / 0.24 ( 42) SS BOND : angle 1.98890 / 1.26 ( 84) hydrogen bonds : bond 0.03440 / 2.23 ( 1046) hydrogen bonds : angle 4.80005 / 3.18 ( 2940) link_BETA1-4 : bond 0.00735 / 0.43 ( 27) link_BETA1-4 : angle 2.08095 / 1.43 ( 81) link_NAG-ASN : bond 0.00375 / 0.22 ( 48) link_NAG-ASN : angle 2.40101 / 1.67 ( 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 375 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 320 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8091 (p90) cc_final: 0.7579 (p90) REVERT: A 160 TYR cc_start: 0.7084 (p90) cc_final: 0.6620 (p90) REVERT: A 197 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6439 (tp) REVERT: A 233 ILE cc_start: 0.6406 (mm) cc_final: 0.6129 (pt) REVERT: A 558 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8536 (mmmt) REVERT: A 737 ASP cc_start: 0.7689 (t0) cc_final: 0.7229 (t70) REVERT: A 869 MET cc_start: 0.8161 (mtt) cc_final: 0.7955 (mtt) REVERT: A 950 ASP cc_start: 0.7933 (m-30) cc_final: 0.7496 (p0) REVERT: A 1111 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7743 (pp20) REVERT: B 142 ASP cc_start: 0.6153 (OUTLIER) cc_final: 0.5914 (m-30) REVERT: B 215 ASP cc_start: 0.7235 (m-30) cc_final: 0.5819 (t0) REVERT: B 221 SER cc_start: 0.9060 (OUTLIER) cc_final: 0.8825 (t) REVERT: B 287 ASP cc_start: 0.8093 (t0) cc_final: 0.7823 (t70) REVERT: B 571 ASP cc_start: 0.7716 (t0) cc_final: 0.7408 (t0) REVERT: B 697 MET cc_start: 0.8579 (ptm) cc_final: 0.8107 (ptt) REVERT: B 725 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7105 (mt-10) REVERT: B 759 PHE cc_start: 0.7255 (m-80) cc_final: 0.6740 (m-10) REVERT: B 918 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8245 (mt-10) REVERT: B 1041 ASP cc_start: 0.8103 (m-30) cc_final: 0.7733 (t0) REVERT: C 558 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8282 (mmtm) REVERT: C 869 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7396 (mtp) REVERT: C 969 LYS cc_start: 0.8468 (ptmm) cc_final: 0.7792 (ttpp) REVERT: C 1050 MET cc_start: 0.8457 (ptm) cc_final: 0.8237 (ptm) REVERT: H 83 MET cc_start: 0.7205 (ptp) cc_final: 0.6322 (mtm) REVERT: H 101 ASP cc_start: 0.7819 (t70) cc_final: 0.7559 (t0) REVERT: L 35 TRP cc_start: 0.6123 (m100) cc_final: 0.5785 (m100) REVERT: L 87 TYR cc_start: 0.7679 (m-80) cc_final: 0.7206 (m-80) REVERT: L 93 ASN cc_start: 0.7662 (t0) cc_final: 0.7391 (t0) REVERT: I 18 LEU cc_start: 0.5335 (mp) cc_final: 0.4979 (mt) REVERT: I 114 GLN cc_start: 0.7947 (mm110) cc_final: 0.7165 (mp10) REVERT: M 4 MET cc_start: 0.5844 (pmm) cc_final: 0.4909 (ptp) REVERT: M 70 ASP cc_start: 0.8552 (p0) cc_final: 0.7971 (m-30) REVERT: J 65 LYS cc_start: 0.6585 (tppt) cc_final: 0.6325 (tppt) REVERT: J 76 LYS cc_start: 0.7930 (mmtt) cc_final: 0.7456 (mmtp) REVERT: J 91 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7040 (t) REVERT: N 55 GLU cc_start: 0.7676 (pm20) cc_final: 0.7260 (pm20) REVERT: N 61 ARG cc_start: 0.7067 (mtp-110) cc_final: 0.6472 (mtm180) REVERT: N 87 TYR cc_start: 0.7114 (m-80) cc_final: 0.6710 (m-80) outliers start: 55 outliers final: 38 residues processed: 364 average time/residue: 0.1632 time to fit residues: 97.2540 Evaluate side-chains 339 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1111 GLU 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 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 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1094 VAL 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 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain I residue 37 VAL 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 103 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 104 optimal weight: 8.9990 chunk 364 optimal weight: 20.0000 chunk 262 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 274 optimal weight: 0.0030 chunk 43 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.188955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119739 restraints weight = 47840.317| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.90 r_work: 0.3280 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31347 Z= 0.131 Angle : 0.625 20.213 42765 Z= 0.306 Chirality : 0.046 0.526 4941 Planarity : 0.004 0.049 5388 Dihedral : 4.442 55.594 4057 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.77 % Favored : 94.12 % Rotamer: Outliers : 1.72 % Allowed : 17.68 % Favored : 80.61 % 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 are not related in a simple way. whole: -0.62 (0.14), residues: 3693 helix: 1.41 (0.21), residues: 656 sheet: -0.15 (0.16), residues: 1082 loop : -1.21 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 38 TYR 0.015 0.001 TYR M 87 PHE 0.028 0.001 PHE L 73 TRP 0.029 0.001 TRP N 35 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (31230) covalent geometry : angle 0.58970 / 0.30 (42456) SS BOND : bond 0.00311 / 0.22 ( 42) SS BOND : angle 2.00908 / 1.27 ( 84) hydrogen bonds : bond 0.03549 / 2.29 ( 1046) hydrogen bonds : angle 4.83609 / 3.20 ( 2940) link_BETA1-4 : bond 0.00706 / 0.40 ( 27) link_BETA1-4 : angle 2.05835 / 1.41 ( 81) link_NAG-ASN : bond 0.00564 / 0.29 ( 48) link_NAG-ASN : angle 2.95966 / 2.07 ( 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 352 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8074 (p90) cc_final: 0.7571 (p90) REVERT: A 160 TYR cc_start: 0.7091 (p90) cc_final: 0.6560 (p90) REVERT: A 197 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6431 (tp) REVERT: A 233 ILE cc_start: 0.6491 (mm) cc_final: 0.6143 (pt) REVERT: A 558 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8510 (mmmt) REVERT: A 586 ASP cc_start: 0.7355 (m-30) cc_final: 0.6892 (m-30) REVERT: A 737 ASP cc_start: 0.7729 (t0) cc_final: 0.7248 (t70) REVERT: A 950 ASP cc_start: 0.7965 (m-30) cc_final: 0.7482 (p0) REVERT: A 1111 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7766 (pp20) REVERT: B 142 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5954 (m-30) REVERT: B 215 ASP cc_start: 0.7307 (m-30) cc_final: 0.5822 (t0) REVERT: B 221 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8844 (t) REVERT: B 287 ASP cc_start: 0.8082 (t0) cc_final: 0.7773 (t70) REVERT: B 697 MET cc_start: 0.8584 (ptm) cc_final: 0.8153 (ptt) REVERT: B 725 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7053 (mt-10) REVERT: B 759 PHE cc_start: 0.7360 (m-80) cc_final: 0.6820 (m-10) REVERT: B 1041 ASP cc_start: 0.8204 (m-30) cc_final: 0.7620 (t0) REVERT: C 558 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8270 (mmtm) REVERT: C 869 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7379 (mtp) REVERT: C 969 LYS cc_start: 0.8479 (ptmm) cc_final: 0.7794 (ttpp) REVERT: C 1050 MET cc_start: 0.8479 (ptm) cc_final: 0.8259 (ptm) REVERT: H 83 MET cc_start: 0.7278 (ptp) cc_final: 0.6396 (mtm) REVERT: H 101 ASP cc_start: 0.7866 (t70) cc_final: 0.7620 (t0) REVERT: L 31 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6489 (p90) REVERT: L 35 TRP cc_start: 0.6179 (m100) cc_final: 0.5887 (m100) REVERT: L 87 TYR cc_start: 0.7682 (m-80) cc_final: 0.7205 (m-80) REVERT: L 93 ASN cc_start: 0.7655 (t0) cc_final: 0.7375 (t0) REVERT: I 18 LEU cc_start: 0.5617 (mp) cc_final: 0.5185 (mt) REVERT: I 114 GLN cc_start: 0.8030 (mm110) cc_final: 0.7216 (mp10) REVERT: M 4 MET cc_start: 0.5732 (pmm) cc_final: 0.4884 (ptp) REVERT: M 70 ASP cc_start: 0.8536 (p0) cc_final: 0.7955 (m-30) REVERT: J 65 LYS cc_start: 0.6522 (tppt) cc_final: 0.6260 (tppt) REVERT: J 76 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7461 (mmtp) REVERT: J 91 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.7005 (t) REVERT: N 35 TRP cc_start: 0.5440 (m100) cc_final: 0.5055 (m100) REVERT: N 36 TYR cc_start: 0.7675 (m-80) cc_final: 0.7019 (m-80) REVERT: N 55 GLU cc_start: 0.7753 (pm20) cc_final: 0.7361 (pm20) outliers start: 56 outliers final: 44 residues processed: 338 average time/residue: 0.1703 time to fit residues: 94.8658 Evaluate side-chains 339 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 207 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1117 THR 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 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 599 THR Chi-restraints excluded: chain B residue 610 VAL 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 312 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL 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 12 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain I residue 37 VAL 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 46 GLU 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 74 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 344 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 209 optimal weight: 5.9990 chunk 319 optimal weight: 30.0000 chunk 342 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 290 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS C 87 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.187845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117226 restraints weight = 47635.914| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.46 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: 0.7493 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31347 Z= 0.135 Angle : 0.637 20.484 42765 Z= 0.312 Chirality : 0.048 0.977 4941 Planarity : 0.004 0.049 5388 Dihedral : 4.439 55.168 4057 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.31 % Rotamer: Outliers : 1.72 % Allowed : 17.89 % Favored : 80.39 % 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 are not related in a simple way. whole: -0.59 (0.14), residues: 3693 helix: 1.43 (0.21), residues: 656 sheet: -0.12 (0.16), residues: 1073 loop : -1.19 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 38 TYR 0.013 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 A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (31230) covalent geometry : angle 0.59600 / 0.30 (42456) SS BOND : bond 0.00353 / 0.25 ( 42) SS BOND : angle 1.88050 / 1.20 ( 84) hydrogen bonds : bond 0.03603 / 2.33 ( 1046) hydrogen bonds : angle 4.81442 / 3.19 ( 2940) link_BETA1-4 : bond 0.00674 / 0.39 ( 27) link_BETA1-4 : angle 2.03526 / 1.40 ( 81) link_NAG-ASN : bond 0.00391 / 0.22 ( 48) link_NAG-ASN : angle 3.38177 / 2.25 ( 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 346 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8104 (p90) cc_final: 0.7606 (p90) REVERT: A 160 TYR cc_start: 0.7073 (p90) cc_final: 0.6543 (p90) REVERT: A 197 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6436 (tp) REVERT: A 233 ILE cc_start: 0.6824 (mm) cc_final: 0.6294 (pt) REVERT: A 542 ASN cc_start: 0.7756 (t0) cc_final: 0.7390 (t0) REVERT: A 558 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8523 (mmmt) REVERT: A 586 ASP cc_start: 0.7403 (m-30) cc_final: 0.6930 (m-30) REVERT: A 737 ASP cc_start: 0.7716 (t0) cc_final: 0.7249 (t70) REVERT: A 904 TYR cc_start: 0.7979 (m-10) cc_final: 0.6804 (m-10) REVERT: A 950 ASP cc_start: 0.7931 (m-30) cc_final: 0.7457 (p0) REVERT: A 1111 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7767 (pp20) REVERT: B 33 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8284 (p) REVERT: B 142 ASP cc_start: 0.6150 (OUTLIER) cc_final: 0.5926 (m-30) REVERT: B 215 ASP cc_start: 0.7290 (m-30) cc_final: 0.5861 (t0) REVERT: B 221 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8848 (t) REVERT: B 287 ASP cc_start: 0.8089 (t0) cc_final: 0.7779 (t70) REVERT: B 697 MET cc_start: 0.8597 (ptm) cc_final: 0.8173 (ptt) REVERT: B 725 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7109 (mt-10) REVERT: B 759 PHE cc_start: 0.7354 (m-80) cc_final: 0.6866 (m-10) REVERT: B 957 GLN cc_start: 0.7643 (mm110) cc_final: 0.7333 (mp10) REVERT: B 1041 ASP cc_start: 0.8176 (m-30) cc_final: 0.7614 (t0) REVERT: C 558 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8277 (mmtm) REVERT: C 869 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7365 (mtp) REVERT: C 969 LYS cc_start: 0.8514 (ptmm) cc_final: 0.7840 (ttpp) REVERT: C 1050 MET cc_start: 0.8448 (ptm) cc_final: 0.8231 (ptm) REVERT: H 83 MET cc_start: 0.7274 (ptp) cc_final: 0.6395 (mtm) REVERT: H 101 ASP cc_start: 0.7874 (t70) cc_final: 0.7633 (t0) REVERT: L 31 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.6521 (p90) REVERT: L 35 TRP cc_start: 0.6192 (m100) cc_final: 0.5936 (m100) REVERT: L 87 TYR cc_start: 0.7681 (m-80) cc_final: 0.7211 (m-80) REVERT: L 93 ASN cc_start: 0.7587 (t0) cc_final: 0.7334 (t0) REVERT: L 103 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7828 (tptt) REVERT: I 6 GLU cc_start: 0.3523 (pm20) cc_final: 0.3018 (pm20) REVERT: I 18 LEU cc_start: 0.5563 (mp) cc_final: 0.5136 (mt) REVERT: I 114 GLN cc_start: 0.8090 (mm110) cc_final: 0.7297 (mp10) REVERT: M 4 MET cc_start: 0.5372 (pmm) cc_final: 0.4337 (ptp) REVERT: M 39 LYS cc_start: 0.6835 (mmtp) cc_final: 0.6206 (ttpp) REVERT: M 70 ASP cc_start: 0.8533 (p0) cc_final: 0.7965 (m-30) REVERT: J 65 LYS cc_start: 0.6298 (tppt) cc_final: 0.5965 (tppt) REVERT: J 76 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7470 (mmtp) REVERT: J 91 THR cc_start: 0.7277 (OUTLIER) cc_final: 0.7032 (t) REVERT: N 35 TRP cc_start: 0.5405 (m100) cc_final: 0.5155 (m100) REVERT: N 55 GLU cc_start: 0.7780 (pm20) cc_final: 0.7221 (pm20) REVERT: N 73 PHE cc_start: 0.7510 (t80) cc_final: 0.7231 (t80) outliers start: 56 outliers final: 43 residues processed: 333 average time/residue: 0.1679 time to fit residues: 91.6949 Evaluate side-chains 338 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 287 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1117 THR 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 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 ASP 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 599 THR Chi-restraints excluded: chain B residue 610 VAL 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 312 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL 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 L residue 31 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain I residue 37 VAL 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 46 GLU 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 74 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: 4.9990 chunk 163 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 86 optimal weight: 0.0020 chunk 291 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 32 optimal weight: 0.0070 chunk 147 optimal weight: 40.0000 overall best weight: 2.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.185734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114573 restraints weight = 48073.274| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.92 r_work: 0.3225 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31347 Z= 0.197 Angle : 0.670 13.274 42765 Z= 0.331 Chirality : 0.048 0.485 4941 Planarity : 0.004 0.049 5388 Dihedral : 4.627 54.152 4057 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 1.72 % Allowed : 17.86 % Favored : 80.42 % 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 are not related in a simple way. whole: -0.70 (0.14), residues: 3693 helix: 1.43 (0.21), residues: 633 sheet: -0.26 (0.16), residues: 1080 loop : -1.23 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 646 TYR 0.020 0.001 TYR B 741 PHE 0.028 0.002 PHE L 73 TRP 0.023 0.002 TRP N 35 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (31230) covalent geometry : angle 0.63882 / 0.32 (42456) SS BOND : bond 0.00375 / 0.26 ( 42) SS BOND : angle 2.10224 / 1.33 ( 84) hydrogen bonds : bond 0.04166 / 2.68 ( 1046) hydrogen bonds : angle 5.01081 / 3.33 ( 2940) link_BETA1-4 : bond 0.00648 / 0.38 ( 27) link_BETA1-4 : angle 2.06432 / 1.41 ( 81) link_NAG-ASN : bond 0.00373 / 0.22 ( 48) link_NAG-ASN : angle 2.81903 / 1.92 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8825.31 seconds wall clock time: 151 minutes 9.36 seconds (9069.36 seconds total)