Starting phenix.real_space_refine on Fri Mar 6 20:26:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fae_31502/03_2026/7fae_31502.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fae_31502/03_2026/7fae_31502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fae_31502/03_2026/7fae_31502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fae_31502/03_2026/7fae_31502.map" model { file = "/net/cci-nas-00/data/ceres_data/7fae_31502/03_2026/7fae_31502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fae_31502/03_2026/7fae_31502.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 144 5.16 5 C 21774 2.51 5 N 5656 2.21 5 O 6778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34352 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 52, 'TRANS': 951} Chain breaks: 8 Chain: "B" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 53, 'TRANS': 952} Chain breaks: 8 Chain: "C" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7866 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 954} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 11, 'TRANS': 210} Chain: "d" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "e" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1666 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "g" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "h" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.91, per 1000 atoms: 0.23 Number of scatterers: 34352 At special positions: 0 Unit cell: (218.25, 188.18, 219.22, 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 144 16.00 O 6778 8.00 N 5656 7.00 C 21774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.17 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.98 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.04 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 88 " distance=2.04 Simple disulfide: pdb=" SG CYS d 134 " - pdb=" SG CYS d 194 " distance=2.04 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 149 " - pdb=" SG CYS e 205 " distance=2.04 Simple disulfide: pdb=" SG CYS g 23 " - pdb=" SG CYS g 88 " distance=2.04 Simple disulfide: pdb=" SG CYS g 134 " - pdb=" SG CYS g 194 " distance=2.04 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS h 149 " - pdb=" SG CYS h 205 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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 C1410 " - " NAG C1411 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 343 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " ASN C 657 " " NAG C1410 " - " ASN C1074 " " NAG E 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN B1134 " Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.4 seconds 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 75 sheets defined 19.6% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.886A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.620A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.811A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.588A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.582A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.717A 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: 3.562A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.354A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.430A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.885A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.620A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.812A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.588A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (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: 3.771A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.633A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.886A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.621A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.812A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.587A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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: 3.965A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.582A 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: 3.664A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'd' and resid 79 through 83 Processing helix chain 'd' and resid 121 through 128 removed outlier: 3.634A pdb=" N GLY d 128 " --> pdb=" O GLN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 189 removed outlier: 3.503A pdb=" N GLU d 187 " --> pdb=" O LYS d 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS d 188 " --> pdb=" O ALA d 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 87 through 91 removed outlier: 3.664A pdb=" N THR e 91 " --> pdb=" O SER e 88 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 140 Processing helix chain 'e' and resid 196 through 198 No H-bonds generated for 'chain 'e' and resid 196 through 198' Processing helix chain 'e' and resid 210 through 213 Processing helix chain 'g' and resid 79 through 83 Processing helix chain 'g' and resid 121 through 128 removed outlier: 3.633A pdb=" N GLY g 128 " --> pdb=" O GLN g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 183 through 189 removed outlier: 3.503A pdb=" N GLU g 187 " --> pdb=" O LYS g 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS g 188 " --> pdb=" O ALA g 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 91 removed outlier: 3.663A pdb=" N THR h 91 " --> pdb=" O SER h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 140 Processing helix chain 'h' and resid 196 through 198 No H-bonds generated for 'chain 'h' and resid 196 through 198' Processing helix chain 'h' and resid 210 through 213 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.633A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.502A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.526A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.757A pdb=" N THR A 274 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 291 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.665A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.618A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.973A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.664A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.879A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.230A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.914A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.688A 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: 4.569A 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: 5.810A 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 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.059A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.618A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.622A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.539A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.649A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.780A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.835A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.626A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.611A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AF2, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.780A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.780A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 159 through 163 removed outlier: 3.558A pdb=" N THR H 160 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS H 205 " --> pdb=" O LYS H 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS H 218 " --> pdb=" O CYS H 205 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 4 through 6 removed outlier: 3.645A pdb=" N VAL d 19 " --> pdb=" O ILE d 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE d 75 " --> pdb=" O VAL d 19 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR d 72 " --> pdb=" O SER d 65 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 10 through 11 Processing sheet with id=AF7, first strand: chain 'd' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP d 35 " --> pdb=" O LEU d 47 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR d 49 " --> pdb=" O LEU d 33 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU d 33 " --> pdb=" O TYR d 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN d 38 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR d 85 " --> pdb=" O GLN d 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'd' and resid 114 through 118 removed outlier: 5.601A pdb=" N TYR d 173 " --> pdb=" O ASN d 138 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 154 through 155 removed outlier: 4.769A pdb=" N TRP d 148 " --> pdb=" O GLN d 155 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 3 through 6 removed outlier: 3.625A pdb=" N GLN e 3 " --> pdb=" O SER e 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER e 25 " --> pdb=" O GLN e 3 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 10 through 12 removed outlier: 6.612A pdb=" N TRP e 36 " --> pdb=" O MET e 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 10 through 12 Processing sheet with id=AG4, first strand: chain 'e' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER e 189 " --> pdb=" O CYS e 149 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR e 185 " --> pdb=" O ASP e 153 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER e 189 " --> pdb=" O CYS e 149 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR e 185 " --> pdb=" O ASP e 153 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'e' and resid 160 through 163 removed outlier: 3.558A pdb=" N THR e 160 " --> pdb=" O ASN e 208 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS e 205 " --> pdb=" O LYS e 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS e 218 " --> pdb=" O CYS e 205 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 4 through 5 removed outlier: 3.645A pdb=" N VAL g 19 " --> pdb=" O ILE g 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE g 75 " --> pdb=" O VAL g 19 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR g 72 " --> pdb=" O SER g 65 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 11 through 13 Processing sheet with id=AG9, first strand: chain 'g' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP g 35 " --> pdb=" O LEU g 47 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR g 49 " --> pdb=" O LEU g 33 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU g 33 " --> pdb=" O TYR g 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN g 38 " --> pdb=" O THR g 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR g 85 " --> pdb=" O GLN g 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'g' and resid 114 through 118 Processing sheet with id=AH2, first strand: chain 'g' and resid 154 through 155 removed outlier: 4.770A pdb=" N TRP g 148 " --> pdb=" O GLN g 155 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 3 through 6 removed outlier: 3.625A pdb=" N GLN h 3 " --> pdb=" O SER h 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER h 25 " --> pdb=" O GLN h 3 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.611A pdb=" N TRP h 36 " --> pdb=" O MET h 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'h' and resid 10 through 12 Processing sheet with id=AH6, first strand: chain 'h' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER h 189 " --> pdb=" O CYS h 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR h 185 " --> pdb=" O ASP h 153 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER h 189 " --> pdb=" O CYS h 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR h 185 " --> pdb=" O ASP h 153 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 160 through 163 removed outlier: 3.868A pdb=" N CYS h 205 " --> pdb=" O LYS h 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS h 218 " --> pdb=" O CYS h 205 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.646A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN L 38 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 114 through 118 Processing sheet with id=AI3, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.769A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 1314 hydrogen bonds defined for protein. 3489 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: 9.31 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6044 1.32 - 1.45: 10852 1.45 - 1.58: 18039 1.58 - 1.72: 0 1.72 - 1.85: 183 Bond restraints: 35118 Sorted by residual: bond pdb=" N THR B 478 " pdb=" CA THR B 478 " ideal model delta sigma weight residual 1.458 1.491 -0.034 7.40e-03 1.83e+04 2.08e+01 bond pdb=" N THR A 478 " pdb=" CA THR A 478 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.99e+01 bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.332 1.388 -0.056 1.34e-02 5.57e+03 1.77e+01 bond pdb=" C HIS C1088 " pdb=" N PHE C1089 " ideal model delta sigma weight residual 1.331 1.265 0.066 1.59e-02 3.96e+03 1.74e+01 bond pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 ... (remaining 35113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 46449 2.69 - 5.39: 1196 5.39 - 8.08: 100 8.08 - 10.77: 10 10.77 - 13.47: 14 Bond angle restraints: 47769 Sorted by residual: angle pdb=" CA PRO L 8 " pdb=" N PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 112.00 98.58 13.42 1.40e+00 5.10e-01 9.19e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 122.26 -11.56 1.22e+00 6.72e-01 8.98e+01 angle pdb=" CA PRO A 899 " pdb=" N PRO A 899 " pdb=" CD PRO A 899 " ideal model delta sigma weight residual 112.00 99.28 12.72 1.40e+00 5.10e-01 8.26e+01 angle pdb=" CA PRO H 158 " pdb=" N PRO H 158 " pdb=" CD PRO H 158 " ideal model delta sigma weight residual 112.00 99.32 12.68 1.40e+00 5.10e-01 8.21e+01 angle pdb=" CA PRO C 899 " pdb=" N PRO C 899 " pdb=" CD PRO C 899 " ideal model delta sigma weight residual 112.00 99.49 12.51 1.40e+00 5.10e-01 7.98e+01 ... (remaining 47764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19076 17.91 - 35.82: 1923 35.82 - 53.73: 497 53.73 - 71.64: 194 71.64 - 89.55: 56 Dihedral angle restraints: 21746 sinusoidal: 9221 harmonic: 12525 Sorted by residual: dihedral pdb=" CA TYR d 94 " pdb=" C TYR d 94 " pdb=" N PRO d 95 " pdb=" CA PRO d 95 " ideal model delta harmonic sigma weight residual -180.00 -113.01 -66.99 0 5.00e+00 4.00e-02 1.80e+02 dihedral pdb=" CA TYR g 94 " pdb=" C TYR g 94 " pdb=" N PRO g 95 " pdb=" CA PRO g 95 " ideal model delta harmonic sigma weight residual -180.00 -113.02 -66.98 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" CA TYR L 94 " pdb=" C TYR L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual -180.00 -113.05 -66.95 0 5.00e+00 4.00e-02 1.79e+02 ... (remaining 21743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5569 0.328 - 0.655: 9 0.655 - 0.983: 3 0.983 - 1.311: 0 1.311 - 1.639: 1 Chirality restraints: 5582 Sorted by residual: chirality pdb=" C1 NAG C1411 " pdb=" O4 NAG C1410 " pdb=" C2 NAG C1411 " pdb=" O5 NAG C1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 5579 not shown) Planarity restraints: 6124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.195 2.00e-02 2.50e+03 2.12e-01 5.62e+02 pdb=" CG ASN A 343 " 0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.351 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.118 5.00e-02 4.00e+02 1.64e-01 4.30e+01 pdb=" N PRO L 8 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 816 " -0.113 5.00e-02 4.00e+02 1.59e-01 4.03e+01 pdb=" N PRO C 817 " 0.274 5.00e-02 4.00e+02 pdb=" CA PRO C 817 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO C 817 " -0.076 5.00e-02 4.00e+02 ... (remaining 6121 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 1 1.81 - 2.58: 411 2.58 - 3.36: 42599 3.36 - 4.13: 80648 4.13 - 4.90: 146395 Nonbonded interactions: 270054 Sorted by model distance: nonbonded pdb=" NH1 ARG A 357 " pdb=" OG1 THR B 167 " model vdw 1.041 3.120 nonbonded pdb=" NH1 ARG A 357 " pdb=" CB THR B 167 " model vdw 1.838 3.550 nonbonded pdb=" O GLN A 804 " pdb=" CD PRO A 817 " model vdw 1.904 3.440 nonbonded pdb=" NH1 ARG A 357 " pdb=" CG2 THR B 167 " model vdw 2.017 3.540 nonbonded pdb=" O PRO H 156 " pdb=" CD PRO H 158 " model vdw 2.040 3.440 ... (remaining 270049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 385 or (resid 386 and (name N or name CA or nam \ e C or name O or name CB )) or resid 387 through 826 or resid 855 through 1408)) \ selection = (chain 'B' and (resid 27 through 385 or (resid 386 and (name N or name CA or nam \ e C or name O or name CB )) or resid 387 through 620 or resid 641 through 939 or \ resid 944 through 1408)) selection = (chain 'C' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1408)) } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = (chain 'H' and (resid 1 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or (resid 158 and (name N or name CA or name C or nam \ e O or name CB )) or resid 159 through 222)) selection = (chain 'e' and (resid 1 through 156 or resid 158 through 222)) selection = (chain 'h' and (resid 1 through 155 or (resid 156 through 158 and (name N or nam \ e CA or name C or name O or name CB )) or resid 159 through 222)) } ncs_group { reference = chain 'L' selection = chain 'd' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.040 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 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 : 0.010 0.231 35231 Z= 0.500 Angle : 1.156 49.058 48057 Z= 0.649 Chirality : 0.071 1.639 5582 Planarity : 0.008 0.164 6080 Dihedral : 16.577 89.552 13547 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.15 % Favored : 90.14 % Rotamer: Outliers : 7.89 % Allowed : 10.58 % Favored : 81.53 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -3.13 (0.11), residues: 4250 helix: -2.21 (0.16), residues: 696 sheet: -1.49 (0.14), residues: 1222 loop : -2.40 (0.11), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1039 TYR 0.038 0.003 TYR H 32 PHE 0.034 0.003 PHE d 71 TRP 0.025 0.003 TRP B 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01026 (35118) covalent geometry : angle 1.03678 (47769) SS BOND : bond 0.02190 ( 51) SS BOND : angle 6.58848 ( 102) hydrogen bonds : bond 0.24085 ( 1213) hydrogen bonds : angle 8.82071 ( 3489) link_BETA1-4 : bond 0.04634 ( 18) link_BETA1-4 : angle 4.61329 ( 54) link_NAG-ASN : bond 0.04043 ( 44) link_NAG-ASN : angle 7.45422 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 642 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 215 ASP cc_start: 0.0880 (OUTLIER) cc_final: 0.0216 (t70) REVERT: A 976 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8447 (m) REVERT: B 369 TYR cc_start: 0.5943 (t80) cc_final: 0.5496 (t80) REVERT: B 697 MET cc_start: 0.8827 (ptm) cc_final: 0.8486 (ptm) REVERT: C 95 THR cc_start: 0.6110 (OUTLIER) cc_final: 0.5829 (m) REVERT: C 158 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5487 (tpt-90) REVERT: C 357 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7704 (tpp-160) REVERT: C 567 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7864 (ptp-170) REVERT: C 786 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7323 (mttm) REVERT: H 180 GLN cc_start: -0.1784 (mt0) cc_final: -0.2846 (tp40) REVERT: d 141 PRO cc_start: 0.5015 (Cg_exo) cc_final: 0.4767 (Cg_endo) REVERT: d 204 PRO cc_start: 0.2173 (Cg_exo) cc_final: 0.1921 (Cg_endo) REVERT: e 81 MET cc_start: 0.3621 (tmm) cc_final: 0.2934 (tpp) REVERT: g 54 LEU cc_start: 0.7990 (tp) cc_final: 0.7670 (mm) REVERT: g 83 PHE cc_start: 0.6353 (m-10) cc_final: 0.5974 (m-80) REVERT: g 140 TYR cc_start: 0.4841 (t80) cc_final: 0.4520 (t80) REVERT: h 72 ARG cc_start: 0.7261 (pmt-80) cc_final: 0.7032 (ptt90) REVERT: h 110 ASP cc_start: 0.6833 (p0) cc_final: 0.6313 (p0) outliers start: 296 outliers final: 54 residues processed: 874 average time/residue: 0.2110 time to fit residues: 296.5735 Evaluate side-chains 329 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 269 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 321 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 606 ASN A 641 ASN A 690 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 901 GLN A 914 ASN A 926 GLN A 969 ASN A 992 GLN A1010 GLN A1071 GLN A1101 HIS A1106 GLN B 134 GLN B 137 ASN B 188 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 644 GLN B 690 GLN B 703 ASN B 856 ASN B 901 GLN B 914 ASN B 926 GLN B 969 ASN B 992 GLN B1005 GLN B1011 GLN C 66 HIS C 115 GLN C 188 ASN C 360 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 501 ASN C 540 ASN C 563 GLN C 690 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 919 ASN C 926 GLN C 992 GLN C1054 GLN C1071 GLN H 57 ASN d 37 GLN e 57 ASN ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 37 GLN h 1 GLN h 57 ASN h 208 ASN L 37 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.127677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.099004 restraints weight = 117370.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.091122 restraints weight = 138203.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089442 restraints weight = 106826.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.087365 restraints weight = 104884.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.087831 restraints weight = 97197.282| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 35231 Z= 0.276 Angle : 0.901 14.154 48057 Z= 0.445 Chirality : 0.053 0.513 5582 Planarity : 0.007 0.118 6080 Dihedral : 8.932 67.045 6010 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.79 % Favored : 94.05 % Rotamer: Outliers : 4.64 % Allowed : 15.03 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.05 % 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: -1.98 (0.12), residues: 4250 helix: -0.35 (0.19), residues: 690 sheet: -0.94 (0.14), residues: 1272 loop : -1.86 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1107 TYR 0.025 0.002 TYR B 200 PHE 0.028 0.003 PHE A 400 TRP 0.047 0.003 TRP d 35 HIS 0.010 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00634 (35118) covalent geometry : angle 0.87543 (47769) SS BOND : bond 0.00601 ( 51) SS BOND : angle 2.23967 ( 102) hydrogen bonds : bond 0.04639 ( 1213) hydrogen bonds : angle 6.48220 ( 3489) link_BETA1-4 : bond 0.00602 ( 18) link_BETA1-4 : angle 2.48543 ( 54) link_NAG-ASN : bond 0.00850 ( 44) link_NAG-ASN : angle 3.41705 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 285 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.1073 (OUTLIER) cc_final: -0.0330 (m) REVERT: A 449 TYR cc_start: 0.6688 (m-80) cc_final: 0.6323 (m-80) REVERT: A 902 MET cc_start: 0.9141 (tpp) cc_final: 0.8698 (tpt) REVERT: A 985 ASP cc_start: 0.6286 (OUTLIER) cc_final: 0.6075 (p0) REVERT: B 369 TYR cc_start: 0.6984 (t80) cc_final: 0.6650 (m-10) REVERT: H 153 ASP cc_start: 0.7258 (m-30) cc_final: 0.7036 (m-30) REVERT: H 180 GLN cc_start: -0.0922 (mt0) cc_final: -0.2709 (tp40) REVERT: e 36 TRP cc_start: 0.4507 (m100) cc_final: 0.3896 (m100) REVERT: e 81 MET cc_start: 0.1679 (tmm) cc_final: 0.1434 (tpp) REVERT: h 72 ARG cc_start: 0.7558 (pmt-80) cc_final: 0.6853 (ptt90) REVERT: h 78 THR cc_start: 0.6597 (OUTLIER) cc_final: 0.6353 (p) REVERT: h 110 ASP cc_start: 0.8376 (p0) cc_final: 0.7653 (p0) REVERT: h 111 TYR cc_start: 0.7979 (m-80) cc_final: 0.7012 (m-80) REVERT: h 154 TYR cc_start: 0.5063 (p90) cc_final: 0.4563 (p90) outliers start: 174 outliers final: 105 residues processed: 444 average time/residue: 0.2029 time to fit residues: 147.4749 Evaluate side-chains 314 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 206 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain g residue 138 ASN Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 221 optimal weight: 0.9980 chunk 382 optimal weight: 40.0000 chunk 63 optimal weight: 1.9990 chunk 350 optimal weight: 40.0000 chunk 134 optimal weight: 10.0000 chunk 427 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 409 optimal weight: 0.4980 chunk 379 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 498 GLN B 580 GLN B 755 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 GLN e 39 GLN ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 138 ASN ** h 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.125206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.096672 restraints weight = 116129.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.087678 restraints weight = 134425.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086377 restraints weight = 112804.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.084900 restraints weight = 105530.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085159 restraints weight = 106312.545| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 35231 Z= 0.261 Angle : 0.785 15.658 48057 Z= 0.384 Chirality : 0.050 0.572 5582 Planarity : 0.006 0.103 6080 Dihedral : 8.043 63.928 5956 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.69 % Rotamer: Outliers : 4.85 % Allowed : 17.08 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.52 (0.12), residues: 4250 helix: 0.58 (0.20), residues: 688 sheet: -0.61 (0.14), residues: 1326 loop : -1.81 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 102 TYR 0.025 0.002 TYR B1067 PHE 0.019 0.002 PHE C 86 TRP 0.031 0.002 TRP h 163 HIS 0.034 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00604 (35118) covalent geometry : angle 0.76038 (47769) SS BOND : bond 0.00488 ( 51) SS BOND : angle 2.03275 ( 102) hydrogen bonds : bond 0.04527 ( 1213) hydrogen bonds : angle 5.97154 ( 3489) link_BETA1-4 : bond 0.00444 ( 18) link_BETA1-4 : angle 2.37555 ( 54) link_NAG-ASN : bond 0.00453 ( 44) link_NAG-ASN : angle 3.07528 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 223 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7117 (t80) REVERT: A 558 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7776 (pttp) REVERT: A 902 MET cc_start: 0.9236 (tpp) cc_final: 0.8698 (tpt) REVERT: C 357 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7590 (tpp-160) REVERT: C 358 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8234 (pt) REVERT: C 484 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: C 979 ASP cc_start: 0.7728 (t70) cc_final: 0.7289 (t0) REVERT: H 153 ASP cc_start: 0.7147 (m-30) cc_final: 0.6946 (m-30) REVERT: H 180 GLN cc_start: -0.1344 (mt0) cc_final: -0.3011 (tp40) REVERT: d 116 PHE cc_start: 0.3770 (m-80) cc_final: 0.2734 (m-80) REVERT: g 83 PHE cc_start: 0.7593 (m-10) cc_final: 0.6883 (m-80) REVERT: g 87 TYR cc_start: 0.7227 (m-80) cc_final: 0.6949 (m-10) REVERT: g 140 TYR cc_start: 0.5277 (t80) cc_final: 0.4871 (t80) REVERT: h 72 ARG cc_start: 0.7771 (pmt-80) cc_final: 0.7078 (ptt90) REVERT: h 104 LEU cc_start: 0.7584 (mp) cc_final: 0.7189 (mt) REVERT: h 110 ASP cc_start: 0.8160 (p0) cc_final: 0.7823 (p0) REVERT: h 153 ASP cc_start: 0.7660 (m-30) cc_final: 0.7144 (p0) REVERT: L 42 LYS cc_start: 0.5010 (OUTLIER) cc_final: 0.4478 (ptmm) REVERT: L 169 LYS cc_start: 0.7218 (pttm) cc_final: 0.6823 (tptp) REVERT: L 188 LYS cc_start: 0.4592 (pttt) cc_final: 0.3702 (mttt) outliers start: 182 outliers final: 110 residues processed: 386 average time/residue: 0.1965 time to fit residues: 125.5738 Evaluate side-chains 302 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 186 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 185 TYR Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 42 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 141 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 223 optimal weight: 0.0870 chunk 370 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 396 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 GLN d 147 GLN ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 208 ASN ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.124536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.095933 restraints weight = 115541.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.086920 restraints weight = 132645.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.085359 restraints weight = 106693.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.084241 restraints weight = 97835.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084522 restraints weight = 95292.585| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 35231 Z= 0.227 Angle : 0.740 15.825 48057 Z= 0.357 Chirality : 0.049 0.542 5582 Planarity : 0.005 0.096 6080 Dihedral : 7.763 63.860 5948 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.45 % Rotamer: Outliers : 4.85 % Allowed : 18.09 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.33 (0.12), residues: 4250 helix: 0.89 (0.20), residues: 693 sheet: -0.55 (0.14), residues: 1345 loop : -1.71 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 328 TYR 0.025 0.002 TYR L 140 PHE 0.024 0.002 PHE C 140 TRP 0.025 0.002 TRP h 163 HIS 0.010 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00530 (35118) covalent geometry : angle 0.71807 (47769) SS BOND : bond 0.00427 ( 51) SS BOND : angle 1.71530 ( 102) hydrogen bonds : bond 0.03972 ( 1213) hydrogen bonds : angle 5.81333 ( 3489) link_BETA1-4 : bond 0.00555 ( 18) link_BETA1-4 : angle 2.20876 ( 54) link_NAG-ASN : bond 0.00390 ( 44) link_NAG-ASN : angle 2.90626 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 201 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7541 (t80) REVERT: A 902 MET cc_start: 0.9178 (tpp) cc_final: 0.8774 (tpt) REVERT: B 229 LEU cc_start: 0.8693 (mt) cc_final: 0.8427 (tp) REVERT: C 357 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7586 (tpp-160) REVERT: C 358 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8198 (pt) REVERT: C 484 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: C 983 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7787 (mtm-85) REVERT: H 81 MET cc_start: 0.2294 (tpp) cc_final: 0.1859 (tpp) REVERT: H 153 ASP cc_start: 0.6931 (m-30) cc_final: 0.6697 (m-30) REVERT: H 180 GLN cc_start: -0.1052 (mt0) cc_final: -0.2818 (tp40) REVERT: d 116 PHE cc_start: 0.3704 (m-80) cc_final: 0.2691 (m-80) REVERT: e 32 TYR cc_start: 0.2466 (OUTLIER) cc_final: 0.2127 (t80) REVERT: e 110 ASP cc_start: 0.5607 (OUTLIER) cc_final: 0.4449 (p0) REVERT: g 18 ARG cc_start: 0.7980 (tmm-80) cc_final: 0.7767 (ttp80) REVERT: g 87 TYR cc_start: 0.7180 (m-80) cc_final: 0.6721 (m-10) REVERT: h 13 LYS cc_start: 0.8414 (ptpp) cc_final: 0.7836 (mmtm) REVERT: h 32 TYR cc_start: 0.5575 (OUTLIER) cc_final: 0.2560 (t80) REVERT: h 72 ARG cc_start: 0.7745 (pmt-80) cc_final: 0.7119 (ptt90) REVERT: h 78 THR cc_start: 0.6431 (OUTLIER) cc_final: 0.6193 (p) REVERT: h 81 MET cc_start: 0.6559 (tmm) cc_final: 0.6267 (tmm) REVERT: L 42 LYS cc_start: 0.5205 (OUTLIER) cc_final: 0.4645 (ptmm) REVERT: L 94 TYR cc_start: 0.3218 (m-10) cc_final: 0.2389 (m-80) REVERT: L 169 LYS cc_start: 0.7116 (pttm) cc_final: 0.6688 (tptp) outliers start: 182 outliers final: 124 residues processed: 362 average time/residue: 0.2022 time to fit residues: 121.1061 Evaluate side-chains 310 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 177 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 32 TYR Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 110 ASP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 40 optimal weight: 30.0000 chunk 364 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 400 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 304 optimal weight: 0.0470 chunk 268 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 121 ASN B 409 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 92 ASN ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.123568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.094615 restraints weight = 115354.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088702 restraints weight = 132948.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085430 restraints weight = 101843.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.084945 restraints weight = 103499.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084913 restraints weight = 98228.866| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 35231 Z= 0.223 Angle : 0.729 16.297 48057 Z= 0.350 Chirality : 0.049 0.530 5582 Planarity : 0.005 0.088 6080 Dihedral : 7.557 62.890 5940 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.09 % Favored : 93.76 % Rotamer: Outliers : 5.33 % Allowed : 18.23 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.18 (0.13), residues: 4250 helix: 1.10 (0.20), residues: 696 sheet: -0.46 (0.14), residues: 1317 loop : -1.62 (0.12), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG g 142 TYR 0.023 0.002 TYR A1067 PHE 0.020 0.002 PHE B 497 TRP 0.016 0.002 TRP h 163 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00521 (35118) covalent geometry : angle 0.71015 (47769) SS BOND : bond 0.00467 ( 51) SS BOND : angle 1.64747 ( 102) hydrogen bonds : bond 0.03895 ( 1213) hydrogen bonds : angle 5.65537 ( 3489) link_BETA1-4 : bond 0.00559 ( 18) link_BETA1-4 : angle 2.16537 ( 54) link_NAG-ASN : bond 0.00423 ( 44) link_NAG-ASN : angle 2.67933 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 199 time to evaluate : 1.221 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 86 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8134 (t80) REVERT: A 902 MET cc_start: 0.9031 (tpp) cc_final: 0.8655 (tpt) REVERT: B 161 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7258 (p) REVERT: B 229 LEU cc_start: 0.8716 (mt) cc_final: 0.8451 (tp) REVERT: B 585 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8845 (pp) REVERT: C 266 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: C 357 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7540 (tpp-160) REVERT: C 474 GLN cc_start: 0.7727 (mt0) cc_final: 0.7258 (tp40) REVERT: C 912 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8718 (p) REVERT: C 977 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8503 (tt) REVERT: H 81 MET cc_start: 0.2322 (tpp) cc_final: 0.2021 (tpp) REVERT: H 153 ASP cc_start: 0.7017 (m-30) cc_final: 0.6744 (m-30) REVERT: H 180 GLN cc_start: -0.1004 (mt0) cc_final: -0.2839 (tp40) REVERT: d 116 PHE cc_start: 0.3552 (m-80) cc_final: 0.2684 (m-80) REVERT: g 18 ARG cc_start: 0.8056 (tmm-80) cc_final: 0.7845 (ttp80) REVERT: g 83 PHE cc_start: 0.7572 (m-10) cc_final: 0.6745 (m-80) REVERT: g 87 TYR cc_start: 0.7192 (m-80) cc_final: 0.6639 (m-10) REVERT: g 106 ILE cc_start: 0.5134 (mt) cc_final: 0.4724 (tp) REVERT: h 13 LYS cc_start: 0.8421 (ptpp) cc_final: 0.7759 (mmtm) REVERT: h 32 TYR cc_start: 0.5643 (OUTLIER) cc_final: 0.2857 (t80) REVERT: h 72 ARG cc_start: 0.7825 (pmt-80) cc_final: 0.7203 (ptt90) REVERT: h 78 THR cc_start: 0.6464 (OUTLIER) cc_final: 0.6220 (p) REVERT: h 108 TYR cc_start: 0.7155 (p90) cc_final: 0.6406 (p90) REVERT: h 110 ASP cc_start: 0.8106 (p0) cc_final: 0.7897 (p0) REVERT: L 42 LYS cc_start: 0.5270 (OUTLIER) cc_final: 0.4686 (ptmm) REVERT: L 94 TYR cc_start: 0.3323 (m-10) cc_final: 0.2767 (m-80) REVERT: L 169 LYS cc_start: 0.7263 (pttm) cc_final: 0.6857 (tptp) outliers start: 200 outliers final: 127 residues processed: 378 average time/residue: 0.2035 time to fit residues: 127.9622 Evaluate side-chains 316 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 179 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 214 optimal weight: 4.9990 chunk 363 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 399 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 275 optimal weight: 0.0770 chunk 293 optimal weight: 0.5980 chunk 403 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 overall best weight: 1.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN B 245 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B1106 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 920 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 37 GLN ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.124396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095022 restraints weight = 114968.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088806 restraints weight = 144391.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.086064 restraints weight = 99259.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.084425 restraints weight = 120413.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084969 restraints weight = 100620.999| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35231 Z= 0.148 Angle : 0.680 16.090 48057 Z= 0.324 Chirality : 0.047 0.507 5582 Planarity : 0.005 0.094 6080 Dihedral : 7.318 64.144 5937 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.64 % Favored : 95.22 % Rotamer: Outliers : 4.40 % Allowed : 19.08 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -0.97 (0.13), residues: 4250 helix: 1.35 (0.21), residues: 693 sheet: -0.33 (0.14), residues: 1330 loop : -1.52 (0.12), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG h 87 TYR 0.034 0.001 TYR d 94 PHE 0.020 0.001 PHE H 106 TRP 0.040 0.002 TRP h 36 HIS 0.008 0.001 HIS g 189 Details of bonding type rmsd covalent geometry : bond 0.00343 (35118) covalent geometry : angle 0.66198 (47769) SS BOND : bond 0.00407 ( 51) SS BOND : angle 1.50265 ( 102) hydrogen bonds : bond 0.03492 ( 1213) hydrogen bonds : angle 5.45690 ( 3489) link_BETA1-4 : bond 0.00626 ( 18) link_BETA1-4 : angle 2.11654 ( 54) link_NAG-ASN : bond 0.00361 ( 44) link_NAG-ASN : angle 2.46364 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 204 time to evaluate : 0.982 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 86 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8201 (t80) REVERT: A 229 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8260 (mt) REVERT: A 902 MET cc_start: 0.9051 (tpp) cc_final: 0.8742 (tpt) REVERT: B 585 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8852 (pp) REVERT: C 357 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7537 (tpp-160) REVERT: C 358 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8142 (pt) REVERT: C 423 TYR cc_start: 0.8276 (t80) cc_final: 0.7667 (t80) REVERT: C 474 GLN cc_start: 0.7771 (mt0) cc_final: 0.7188 (tp40) REVERT: C 912 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8731 (p) REVERT: C 977 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8560 (tt) REVERT: H 48 MET cc_start: 0.6708 (mtp) cc_final: 0.6486 (ptp) REVERT: H 70 ILE cc_start: 0.0253 (OUTLIER) cc_final: -0.0617 (pt) REVERT: H 153 ASP cc_start: 0.7129 (m-30) cc_final: 0.6768 (m-30) REVERT: H 180 GLN cc_start: -0.0714 (mt0) cc_final: -0.2897 (tp40) REVERT: d 116 PHE cc_start: 0.3751 (m-80) cc_final: 0.2741 (m-80) REVERT: e 180 GLN cc_start: -0.3082 (mt0) cc_final: -0.4199 (mm-40) REVERT: g 83 PHE cc_start: 0.7747 (m-10) cc_final: 0.6974 (m-80) REVERT: g 87 TYR cc_start: 0.7284 (m-80) cc_final: 0.6636 (m-10) REVERT: h 13 LYS cc_start: 0.8326 (ptpp) cc_final: 0.7628 (mmtm) REVERT: h 32 TYR cc_start: 0.5636 (OUTLIER) cc_final: 0.3215 (t80) REVERT: h 72 ARG cc_start: 0.7872 (pmt-80) cc_final: 0.7302 (ptt90) REVERT: h 78 THR cc_start: 0.6295 (OUTLIER) cc_final: 0.6029 (p) REVERT: L 42 LYS cc_start: 0.5327 (OUTLIER) cc_final: 0.4817 (ptmm) REVERT: L 169 LYS cc_start: 0.7269 (pttm) cc_final: 0.6910 (tptp) REVERT: L 190 LYS cc_start: 0.6521 (tptp) cc_final: 0.5906 (ptmt) outliers start: 165 outliers final: 119 residues processed: 350 average time/residue: 0.1994 time to fit residues: 116.4568 Evaluate side-chains 319 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 189 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 85 optimal weight: 7.9990 chunk 359 optimal weight: 40.0000 chunk 40 optimal weight: 0.2980 chunk 394 optimal weight: 10.0000 chunk 416 optimal weight: 6.9990 chunk 378 optimal weight: 8.9990 chunk 284 optimal weight: 0.9990 chunk 233 optimal weight: 0.0060 chunk 224 optimal weight: 3.9990 chunk 300 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 overall best weight: 2.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 6 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.123775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.094571 restraints weight = 115606.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.087672 restraints weight = 149364.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085698 restraints weight = 103168.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.084214 restraints weight = 110630.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.084561 restraints weight = 109932.290| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35231 Z= 0.174 Angle : 0.685 16.008 48057 Z= 0.327 Chirality : 0.047 0.508 5582 Planarity : 0.005 0.101 6080 Dihedral : 7.207 64.514 5936 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.45 % Rotamer: Outliers : 4.53 % Allowed : 19.37 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -0.91 (0.13), residues: 4250 helix: 1.47 (0.20), residues: 693 sheet: -0.34 (0.14), residues: 1347 loop : -1.47 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.032 0.001 TYR d 94 PHE 0.016 0.001 PHE C 86 TRP 0.024 0.001 TRP h 36 HIS 0.006 0.001 HIS g 189 Details of bonding type rmsd covalent geometry : bond 0.00408 (35118) covalent geometry : angle 0.66643 (47769) SS BOND : bond 0.00378 ( 51) SS BOND : angle 1.67679 ( 102) hydrogen bonds : bond 0.03554 ( 1213) hydrogen bonds : angle 5.42323 ( 3489) link_BETA1-4 : bond 0.00574 ( 18) link_BETA1-4 : angle 2.07585 ( 54) link_NAG-ASN : bond 0.00358 ( 44) link_NAG-ASN : angle 2.47691 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 201 time to evaluate : 1.335 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 229 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8262 (mt) REVERT: A 902 MET cc_start: 0.8949 (tpp) cc_final: 0.8595 (tpt) REVERT: B 161 SER cc_start: 0.8112 (OUTLIER) cc_final: 0.7265 (p) REVERT: B 585 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8830 (pp) REVERT: C 357 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7493 (tpp-160) REVERT: C 440 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8313 (p0) REVERT: C 977 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8585 (tt) REVERT: H 48 MET cc_start: 0.6895 (mtp) cc_final: 0.6672 (ptp) REVERT: H 70 ILE cc_start: 0.0090 (OUTLIER) cc_final: -0.1033 (pt) REVERT: H 153 ASP cc_start: 0.6902 (m-30) cc_final: 0.6500 (m-30) REVERT: H 180 GLN cc_start: -0.0672 (mt0) cc_final: -0.2789 (tp40) REVERT: d 116 PHE cc_start: 0.3605 (m-80) cc_final: 0.2702 (m-80) REVERT: e 13 LYS cc_start: 0.3229 (mmtt) cc_final: 0.3017 (mmpt) REVERT: e 32 TYR cc_start: 0.2025 (OUTLIER) cc_final: 0.1744 (t80) REVERT: g 83 PHE cc_start: 0.7682 (m-10) cc_final: 0.6906 (m-80) REVERT: g 87 TYR cc_start: 0.7219 (m-80) cc_final: 0.6719 (m-10) REVERT: h 13 LYS cc_start: 0.8327 (ptpp) cc_final: 0.7632 (mmtm) REVERT: h 32 TYR cc_start: 0.5807 (OUTLIER) cc_final: 0.3278 (t80) REVERT: h 72 ARG cc_start: 0.7889 (pmt-80) cc_final: 0.7655 (ppt170) REVERT: h 78 THR cc_start: 0.6391 (OUTLIER) cc_final: 0.6169 (p) REVERT: h 164 ASN cc_start: 0.7172 (m-40) cc_final: 0.5994 (t0) REVERT: L 42 LYS cc_start: 0.5370 (OUTLIER) cc_final: 0.4867 (ptmm) REVERT: L 169 LYS cc_start: 0.7287 (pttm) cc_final: 0.6998 (tptp) REVERT: L 190 LYS cc_start: 0.6541 (tptp) cc_final: 0.5965 (ptmt) outliers start: 170 outliers final: 132 residues processed: 358 average time/residue: 0.2014 time to fit residues: 119.6168 Evaluate side-chains 323 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 180 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 32 TYR Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 202 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain g residue 138 ASN Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 343 optimal weight: 0.0970 chunk 303 optimal weight: 40.0000 chunk 290 optimal weight: 0.9980 chunk 378 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 411 optimal weight: 30.0000 chunk 16 optimal weight: 4.9990 chunk 385 optimal weight: 20.0000 overall best weight: 2.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 6 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.123584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.094961 restraints weight = 118234.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088394 restraints weight = 137893.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.085614 restraints weight = 106787.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.083947 restraints weight = 113239.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084560 restraints weight = 111223.132| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35231 Z= 0.177 Angle : 0.687 16.185 48057 Z= 0.328 Chirality : 0.047 0.508 5582 Planarity : 0.005 0.105 6080 Dihedral : 7.085 60.562 5934 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.13 % Favored : 94.75 % Rotamer: Outliers : 4.45 % Allowed : 19.80 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -0.86 (0.13), residues: 4250 helix: 1.52 (0.20), residues: 690 sheet: -0.31 (0.14), residues: 1353 loop : -1.44 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 61 TYR 0.022 0.001 TYR A1067 PHE 0.020 0.002 PHE A 140 TRP 0.021 0.001 TRP h 36 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00417 (35118) covalent geometry : angle 0.67024 (47769) SS BOND : bond 0.00443 ( 51) SS BOND : angle 1.62475 ( 102) hydrogen bonds : bond 0.03547 ( 1213) hydrogen bonds : angle 5.34303 ( 3489) link_BETA1-4 : bond 0.00554 ( 18) link_BETA1-4 : angle 2.01634 ( 54) link_NAG-ASN : bond 0.00339 ( 44) link_NAG-ASN : angle 2.38473 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 197 time to evaluate : 1.160 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 229 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8367 (mt) REVERT: A 902 MET cc_start: 0.8959 (tpp) cc_final: 0.8646 (tpt) REVERT: B 161 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7381 (p) REVERT: B 585 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8862 (pp) REVERT: C 357 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7463 (tpp-160) REVERT: C 440 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8314 (p0) REVERT: C 869 MET cc_start: 0.8771 (mtm) cc_final: 0.8502 (mtt) REVERT: C 977 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8585 (tt) REVERT: H 48 MET cc_start: 0.6968 (mtp) cc_final: 0.6751 (ptp) REVERT: H 70 ILE cc_start: 0.0236 (OUTLIER) cc_final: -0.0715 (pt) REVERT: d 91 TYR cc_start: 0.0293 (OUTLIER) cc_final: -0.0205 (p90) REVERT: d 116 PHE cc_start: 0.3612 (m-80) cc_final: 0.2671 (m-80) REVERT: e 32 TYR cc_start: 0.2089 (OUTLIER) cc_final: 0.1834 (t80) REVERT: g 87 TYR cc_start: 0.7313 (m-80) cc_final: 0.6802 (m-10) REVERT: h 13 LYS cc_start: 0.8334 (ptpp) cc_final: 0.7617 (mmtm) REVERT: h 32 TYR cc_start: 0.5868 (OUTLIER) cc_final: 0.3462 (t80) REVERT: h 72 ARG cc_start: 0.7985 (pmt-80) cc_final: 0.7610 (ppt170) REVERT: h 164 ASN cc_start: 0.7282 (m-40) cc_final: 0.6275 (t0) REVERT: L 42 LYS cc_start: 0.5455 (OUTLIER) cc_final: 0.4975 (ptmm) REVERT: L 55 GLU cc_start: 0.5646 (tp30) cc_final: 0.5436 (tp30) REVERT: L 91 TYR cc_start: 0.2648 (OUTLIER) cc_final: 0.1926 (p90) REVERT: L 169 LYS cc_start: 0.7306 (pttm) cc_final: 0.7063 (tptp) REVERT: L 188 LYS cc_start: 0.4149 (pttt) cc_final: 0.3257 (mttt) REVERT: L 190 LYS cc_start: 0.6542 (tptp) cc_final: 0.6001 (ptmt) outliers start: 167 outliers final: 137 residues processed: 348 average time/residue: 0.2006 time to fit residues: 116.5933 Evaluate side-chains 333 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 184 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 91 TYR Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 32 TYR Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 202 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 138 ASN Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 109 PHE Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 217 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 301 optimal weight: 4.9990 chunk 420 optimal weight: 5.9990 chunk 428 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 321 optimal weight: 0.7980 chunk 355 optimal weight: 30.0000 chunk 303 optimal weight: 6.9990 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.123339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.095455 restraints weight = 117701.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.086016 restraints weight = 130397.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.083086 restraints weight = 108148.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.083087 restraints weight = 92684.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083370 restraints weight = 84436.779| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35231 Z= 0.177 Angle : 0.686 16.031 48057 Z= 0.326 Chirality : 0.047 0.508 5582 Planarity : 0.005 0.105 6080 Dihedral : 6.996 63.473 5933 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 4.50 % Allowed : 20.01 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -0.84 (0.13), residues: 4250 helix: 1.44 (0.20), residues: 708 sheet: -0.29 (0.14), residues: 1343 loop : -1.41 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 328 TYR 0.027 0.001 TYR d 94 PHE 0.016 0.001 PHE C 86 TRP 0.018 0.001 TRP h 36 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00417 (35118) covalent geometry : angle 0.66910 (47769) SS BOND : bond 0.00432 ( 51) SS BOND : angle 1.57231 ( 102) hydrogen bonds : bond 0.03540 ( 1213) hydrogen bonds : angle 5.30787 ( 3489) link_BETA1-4 : bond 0.00578 ( 18) link_BETA1-4 : angle 1.98297 ( 54) link_NAG-ASN : bond 0.00350 ( 44) link_NAG-ASN : angle 2.39791 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 194 time to evaluate : 1.313 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 229 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8374 (mt) REVERT: A 902 MET cc_start: 0.9045 (tpp) cc_final: 0.8819 (tpt) REVERT: B 161 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7386 (p) REVERT: B 380 TYR cc_start: 0.4601 (OUTLIER) cc_final: 0.3210 (m-80) REVERT: B 515 PHE cc_start: 0.7843 (m-10) cc_final: 0.7277 (m-10) REVERT: B 585 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8860 (pp) REVERT: C 319 ARG cc_start: 0.7371 (mtp-110) cc_final: 0.7095 (ttm-80) REVERT: C 357 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7441 (tpp-160) REVERT: C 440 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8309 (p0) REVERT: C 660 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: H 48 MET cc_start: 0.6965 (mtp) cc_final: 0.6736 (ptp) REVERT: H 70 ILE cc_start: 0.0146 (OUTLIER) cc_final: -0.0801 (pt) REVERT: H 180 GLN cc_start: -0.1416 (mt0) cc_final: -0.3347 (tp40) REVERT: d 91 TYR cc_start: 0.0153 (OUTLIER) cc_final: -0.0459 (p90) REVERT: d 116 PHE cc_start: 0.3507 (m-80) cc_final: 0.2611 (m-80) REVERT: e 32 TYR cc_start: 0.1990 (OUTLIER) cc_final: 0.1757 (t80) REVERT: g 87 TYR cc_start: 0.7326 (m-80) cc_final: 0.6751 (m-10) REVERT: h 13 LYS cc_start: 0.8362 (ptpp) cc_final: 0.7639 (mmtm) REVERT: h 32 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.4020 (m-80) REVERT: h 72 ARG cc_start: 0.8083 (pmt-80) cc_final: 0.7735 (ppt170) REVERT: h 164 ASN cc_start: 0.7283 (m-40) cc_final: 0.6225 (t0) REVERT: L 42 LYS cc_start: 0.5435 (OUTLIER) cc_final: 0.4923 (ptmm) REVERT: L 91 TYR cc_start: 0.2860 (OUTLIER) cc_final: 0.1956 (p90) REVERT: L 188 LYS cc_start: 0.4108 (pttt) cc_final: 0.3233 (mttt) REVERT: L 190 LYS cc_start: 0.6542 (tptp) cc_final: 0.6010 (ptmt) outliers start: 169 outliers final: 139 residues processed: 346 average time/residue: 0.2038 time to fit residues: 117.3592 Evaluate side-chains 334 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 182 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 91 TYR Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 32 TYR Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 202 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 109 PHE Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 167 optimal weight: 2.9990 chunk 304 optimal weight: 0.0870 chunk 428 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 320 optimal weight: 20.0000 chunk 256 optimal weight: 0.5980 chunk 423 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 351 optimal weight: 7.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 409 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.124495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095924 restraints weight = 118759.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.089064 restraints weight = 142178.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.086717 restraints weight = 98781.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084642 restraints weight = 118090.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085124 restraints weight = 100864.262| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35231 Z= 0.119 Angle : 0.661 16.324 48057 Z= 0.314 Chirality : 0.046 0.477 5582 Planarity : 0.005 0.110 6080 Dihedral : 6.727 63.874 5930 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.42 % Favored : 95.46 % Rotamer: Outliers : 3.28 % Allowed : 21.40 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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 (0.13), residues: 4250 helix: 1.55 (0.20), residues: 712 sheet: -0.18 (0.14), residues: 1322 loop : -1.33 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG h 103 TYR 0.034 0.001 TYR L 94 PHE 0.017 0.001 PHE A 140 TRP 0.022 0.001 TRP h 36 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00276 (35118) covalent geometry : angle 0.64598 (47769) SS BOND : bond 0.00403 ( 51) SS BOND : angle 1.42751 ( 102) hydrogen bonds : bond 0.03199 ( 1213) hydrogen bonds : angle 5.13628 ( 3489) link_BETA1-4 : bond 0.00600 ( 18) link_BETA1-4 : angle 1.96198 ( 54) link_NAG-ASN : bond 0.00342 ( 44) link_NAG-ASN : angle 2.23628 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 196 time to evaluate : 0.955 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 229 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8178 (mt) REVERT: A 386 LYS cc_start: 0.8893 (mttt) cc_final: 0.8592 (mmmt) REVERT: B 380 TYR cc_start: 0.4821 (OUTLIER) cc_final: 0.3444 (m-80) REVERT: C 269 TYR cc_start: 0.6733 (m-80) cc_final: 0.6475 (m-80) REVERT: C 319 ARG cc_start: 0.7196 (mtp-110) cc_final: 0.6944 (ttm-80) REVERT: C 357 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7417 (tpp-160) REVERT: C 440 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8322 (p0) REVERT: H 48 MET cc_start: 0.6903 (mtp) cc_final: 0.6673 (ptp) REVERT: H 70 ILE cc_start: 0.0119 (OUTLIER) cc_final: -0.0843 (pt) REVERT: H 180 GLN cc_start: -0.1145 (mt0) cc_final: -0.3171 (tp40) REVERT: d 91 TYR cc_start: 0.0072 (OUTLIER) cc_final: -0.0507 (p90) REVERT: d 116 PHE cc_start: 0.3602 (m-80) cc_final: 0.2653 (m-80) REVERT: g 87 TYR cc_start: 0.7329 (m-80) cc_final: 0.6612 (m-10) REVERT: h 32 TYR cc_start: 0.5859 (OUTLIER) cc_final: 0.4032 (m-80) REVERT: h 164 ASN cc_start: 0.7449 (m-40) cc_final: 0.6371 (t0) REVERT: L 91 TYR cc_start: 0.2680 (OUTLIER) cc_final: 0.1874 (p90) REVERT: L 188 LYS cc_start: 0.4033 (pttt) cc_final: 0.3193 (mttt) REVERT: L 190 LYS cc_start: 0.6640 (tptp) cc_final: 0.6098 (ptmt) outliers start: 123 outliers final: 93 residues processed: 307 average time/residue: 0.1997 time to fit residues: 101.7667 Evaluate side-chains 279 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 178 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 91 TYR Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 202 THR Chi-restraints excluded: chain g residue 61 ARG Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 322 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 379 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 302 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 397 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 305 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.124531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.096402 restraints weight = 117567.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.089291 restraints weight = 134543.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.087097 restraints weight = 102187.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084859 restraints weight = 97588.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084909 restraints weight = 97344.849| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35231 Z= 0.121 Angle : 0.656 16.274 48057 Z= 0.311 Chirality : 0.046 0.472 5582 Planarity : 0.005 0.110 6080 Dihedral : 6.564 62.859 5928 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.73 % Favored : 95.15 % Rotamer: Outliers : 3.04 % Allowed : 21.77 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -0.63 (0.13), residues: 4250 helix: 1.63 (0.20), residues: 712 sheet: -0.10 (0.14), residues: 1317 loop : -1.32 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG h 103 TYR 0.025 0.001 TYR A 351 PHE 0.021 0.001 PHE g 62 TRP 0.019 0.001 TRP h 36 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00282 (35118) covalent geometry : angle 0.64141 (47769) SS BOND : bond 0.00397 ( 51) SS BOND : angle 1.39488 ( 102) hydrogen bonds : bond 0.03146 ( 1213) hydrogen bonds : angle 5.06958 ( 3489) link_BETA1-4 : bond 0.00607 ( 18) link_BETA1-4 : angle 1.94076 ( 54) link_NAG-ASN : bond 0.00324 ( 44) link_NAG-ASN : angle 2.21112 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7060.33 seconds wall clock time: 122 minutes 9.20 seconds (7329.20 seconds total)