Starting phenix.real_space_refine on Wed Apr 8 04:29:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7czv_30518/04_2026/7czv_30518.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czv_30518/04_2026/7czv_30518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7czv_30518/04_2026/7czv_30518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czv_30518/04_2026/7czv_30518.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7czv_30518/04_2026/7czv_30518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czv_30518/04_2026/7czv_30518.map" } resolution = 3.3 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= 0.006 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 147 5.16 5 C 21960 2.51 5 N 5685 2.21 5 O 6880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34672 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "K" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "I" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "M" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "J" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 8.59, per 1000 atoms: 0.25 Number of scatterers: 34672 At special positions: 0 Unit cell: (147.832, 171.746, 238.053, 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 147 16.00 O 6880 8.00 N 5685 7.00 C 21960 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.17 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=2.11 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.14 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.09 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=2.32 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.08 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.08 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.10 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.55 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.55 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 154 " - pdb=" SG CYS J 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.56 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A1406 " - " NAG A1407 " " NAG B1409 " - " NAG B1410 " " NAG C1406 " - " NAG C1407 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 331 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B1074 " " 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 331 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 616 " " NAG C1410 " - " ASN C 657 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 709 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.4 seconds 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8108 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 79 sheets defined 17.9% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.632A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.770A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.636A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.645A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.627A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.648A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.601A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.371A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.583A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'I' and resid 201 through 203 No H-bonds generated for 'chain 'I' and resid 201 through 203' Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing helix chain 'J' and resid 201 through 203 No H-bonds generated for 'chain 'J' and resid 201 through 203' Processing helix chain 'N' and resid 121 through 128 Processing helix chain 'N' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.680A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.336A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.609A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.516A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN B 280 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE B 285 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.820A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.654A 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) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.577A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 55 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 208 through 209 removed outlier: 3.557A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.534A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 132 through 135 removed outlier: 4.139A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 193 through 194 removed outlier: 5.992A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 275 through 279 removed outlier: 3.888A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.118A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.605A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AF7, first strand: chain 'H' and resid 46 through 51 removed outlier: 6.652A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 164 through 168 Processing sheet with id=AG2, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AG3, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.680A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN K 38 " --> pdb=" O THR K 85 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 114 through 118 Processing sheet with id=AG5, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG6, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AG7, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AG8, first strand: chain 'I' and resid 46 through 51 removed outlier: 6.652A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA I 151 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 198 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 153 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 196 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 155 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER I 194 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 157 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU I 192 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA I 151 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 198 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 153 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 196 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 155 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER I 194 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 157 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU I 192 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 164 through 168 Processing sheet with id=AH3, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AH4, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.680A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN M 38 " --> pdb=" O THR M 85 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 114 through 118 Processing sheet with id=AH6, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AH7, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AH8, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AH9, first strand: chain 'J' and resid 46 through 51 removed outlier: 6.652A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA J 151 " --> pdb=" O VAL J 198 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 198 " --> pdb=" O ALA J 151 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 153 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 196 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU J 155 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 194 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 157 " --> pdb=" O LEU J 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 192 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA J 151 " --> pdb=" O VAL J 198 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 198 " --> pdb=" O ALA J 151 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 153 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 196 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU J 155 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 194 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 157 " --> pdb=" O LEU J 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 192 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 164 through 168 Processing sheet with id=AI4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AI5, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.679A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN N 38 " --> pdb=" O THR N 85 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AI7, first strand: chain 'N' and resid 153 through 154 1220 hydrogen bonds defined for protein. 3210 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: 8.87 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5801 1.32 - 1.45: 10417 1.45 - 1.58: 19019 1.58 - 1.71: 3 1.71 - 1.85: 186 Bond restraints: 35426 Sorted by residual: bond pdb=" CA HIS B 49 " pdb=" C HIS B 49 " ideal model delta sigma weight residual 1.520 1.406 0.115 1.22e-02 6.72e+03 8.88e+01 bond pdb=" CA GLN C 239 " pdb=" C GLN C 239 " ideal model delta sigma weight residual 1.525 1.421 0.104 1.11e-02 8.12e+03 8.85e+01 bond pdb=" CA ASN C 30 " pdb=" C ASN C 30 " ideal model delta sigma weight residual 1.520 1.415 0.105 1.16e-02 7.43e+03 8.15e+01 bond pdb=" CA TYR B 204 " pdb=" C TYR B 204 " ideal model delta sigma weight residual 1.523 1.421 0.102 1.18e-02 7.18e+03 7.46e+01 bond pdb=" CA ARG C 44 " pdb=" C ARG C 44 " ideal model delta sigma weight residual 1.521 1.414 0.107 1.24e-02 6.50e+03 7.42e+01 ... (remaining 35421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 46129 2.75 - 5.51: 1711 5.51 - 8.26: 273 8.26 - 11.02: 51 11.02 - 13.77: 22 Bond angle restraints: 48186 Sorted by residual: angle pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " pdb=" CG PHE C 32 " ideal model delta sigma weight residual 113.80 103.52 10.28 1.00e+00 1.00e+00 1.06e+02 angle pdb=" CA GLN C 271 " pdb=" C GLN C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 117.82 125.24 -7.42 7.80e-01 1.64e+00 9.04e+01 angle pdb=" CA GLU C 224 " pdb=" C GLU C 224 " pdb=" O GLU C 224 " ideal model delta sigma weight residual 120.19 112.60 7.59 8.40e-01 1.42e+00 8.17e+01 angle pdb=" CA ASN B 188 " pdb=" CB ASN B 188 " pdb=" CG ASN B 188 " ideal model delta sigma weight residual 112.60 103.64 8.96 1.00e+00 1.00e+00 8.02e+01 angle pdb=" CA PHE C 238 " pdb=" CB PHE C 238 " pdb=" CG PHE C 238 " ideal model delta sigma weight residual 113.80 122.38 -8.58 1.00e+00 1.00e+00 7.37e+01 ... (remaining 48181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19066 17.91 - 35.83: 2131 35.83 - 53.74: 615 53.74 - 71.66: 207 71.66 - 89.57: 62 Dihedral angle restraints: 22081 sinusoidal: 9462 harmonic: 12619 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 35.69 57.31 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CA ASP B 198 " pdb=" CB ASP B 198 " ideal model delta harmonic sigma weight residual 122.80 138.64 -15.84 0 2.50e+00 1.60e-01 4.02e+01 ... (remaining 22078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5629 0.328 - 0.656: 30 0.656 - 0.984: 5 0.984 - 1.312: 3 1.312 - 1.640: 3 Chirality restraints: 5670 Sorted by residual: chirality pdb=" C1 NAG C1407 " pdb=" O4 NAG C1406 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -3.44 1.04 2.00e-02 2.50e+03 2.72e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.65e+02 ... (remaining 5667 not shown) Planarity restraints: 6185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.190 2.00e-02 2.50e+03 2.35e-01 6.93e+02 pdb=" CG ASN C 657 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.388 2.00e-02 2.50e+03 pdb=" C1 NAG C1410 " -0.291 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " -0.041 2.00e-02 2.50e+03 2.27e-01 6.47e+02 pdb=" CG ASN B 122 " 0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " -0.167 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " 0.401 2.00e-02 2.50e+03 pdb=" C1 NAG B1402 " -0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 122 " 0.074 2.00e-02 2.50e+03 2.03e-01 5.14e+02 pdb=" CG ASN C 122 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN C 122 " 0.113 2.00e-02 2.50e+03 pdb=" ND2 ASN C 122 " -0.361 2.00e-02 2.50e+03 pdb=" C1 NAG C1402 " 0.232 2.00e-02 2.50e+03 ... (remaining 6182 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 392 2.51 - 3.11: 25755 3.11 - 3.71: 50214 3.71 - 4.30: 74604 4.30 - 4.90: 124209 Nonbonded interactions: 275174 Sorted by model distance: nonbonded pdb=" O ARG C 273 " pdb=" OG1 THR C 274 " model vdw 1.913 3.040 nonbonded pdb=" O ASP I 62 " pdb=" OG SER I 63 " model vdw 1.945 3.040 nonbonded pdb=" O ASP H 62 " pdb=" OG SER H 63 " model vdw 1.945 3.040 nonbonded pdb=" O ASP J 62 " pdb=" OG SER J 63 " model vdw 1.945 3.040 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.982 3.120 ... (remaining 275169 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 620 or resid 641 through 939 or resid 944 throu \ gh 1410)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1410)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1410)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.840 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 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 : 0.014 0.524 35548 Z= 0.726 Angle : 1.547 56.815 48501 Z= 0.834 Chirality : 0.089 1.640 5670 Planarity : 0.009 0.185 6137 Dihedral : 17.446 89.571 13820 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 31.71 Ramachandran Plot: Outliers : 2.94 % Allowed : 11.36 % Favored : 85.70 % Rotamer: Outliers : 11.76 % Allowed : 16.17 % Favored : 72.07 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.11), residues: 4280 helix: -2.26 (0.16), residues: 683 sheet: -1.88 (0.13), residues: 1364 loop : -3.22 (0.11), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 44 TYR 0.091 0.003 TYR C 38 PHE 0.119 0.005 PHE C 220 TRP 0.166 0.005 TRP C 64 HIS 0.008 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01220 (35426) covalent geometry : angle 1.26426 (48186) SS BOND : bond 0.13844 ( 51) SS BOND : angle 11.16161 ( 102) hydrogen bonds : bond 0.21392 ( 1142) hydrogen bonds : angle 8.64297 ( 3210) link_BETA1-4 : bond 0.10090 ( 23) link_BETA1-4 : angle 10.34250 ( 69) link_NAG-ASN : bond 0.03727 ( 48) link_NAG-ASN : angle 11.45589 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 445 poor density : 678 time to evaluate : 1.275 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: A 153 MET cc_start: 0.0165 (mpp) cc_final: -0.0868 (ttp) REVERT: A 517 LEU cc_start: 0.4391 (OUTLIER) cc_final: 0.3837 (pt) REVERT: A 572 THR cc_start: 0.7423 (p) cc_final: 0.6956 (p) REVERT: A 886 TRP cc_start: 0.5457 (p90) cc_final: 0.5076 (p90) REVERT: A 902 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5748 (tpt) REVERT: A 988 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.4879 (tp30) REVERT: B 197 ILE cc_start: 0.6595 (mm) cc_final: 0.6310 (tt) REVERT: B 529 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.4921 (mmtt) REVERT: B 547 THR cc_start: 0.6455 (m) cc_final: 0.6208 (p) REVERT: B 606 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.6527 (t0) REVERT: B 676 THR cc_start: 0.6071 (OUTLIER) cc_final: 0.5799 (m) REVERT: B 1094 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7288 (m) REVERT: C 770 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6435 (pt) REVERT: C 856 ASN cc_start: 0.6752 (OUTLIER) cc_final: 0.6386 (p0) REVERT: C 973 ILE cc_start: 0.7510 (pt) cc_final: 0.7307 (pt) REVERT: H 107 GLN cc_start: 0.2780 (OUTLIER) cc_final: 0.2575 (mt0) REVERT: H 193 SER cc_start: 0.0623 (OUTLIER) cc_final: 0.0362 (p) REVERT: I 83 MET cc_start: -0.0083 (mtm) cc_final: -0.1013 (tmm) REVERT: I 105 MET cc_start: 0.0957 (mtp) cc_final: 0.0538 (mpp) REVERT: I 209 ILE cc_start: 0.3104 (OUTLIER) cc_final: 0.2599 (tp) REVERT: M 6 GLN cc_start: 0.4252 (mt0) cc_final: 0.3450 (tp40) REVERT: J 107 GLN cc_start: 0.6002 (OUTLIER) cc_final: 0.5758 (mm110) REVERT: J 217 SER cc_start: 0.0036 (OUTLIER) cc_final: -0.0339 (t) REVERT: N 27 GLN cc_start: 0.0774 (pm20) cc_final: 0.0488 (pt0) REVERT: N 50 ASP cc_start: 0.5056 (OUTLIER) cc_final: 0.4258 (p0) REVERT: N 65 SER cc_start: 0.4971 (t) cc_final: 0.4622 (m) REVERT: N 103 LYS cc_start: 0.4625 (tptp) cc_final: 0.4190 (mttt) outliers start: 445 outliers final: 84 residues processed: 1032 average time/residue: 0.2031 time to fit residues: 348.1194 Evaluate side-chains 430 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 331 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 217 PRO Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 159 SER Chi-restraints excluded: chain J residue 107 GLN Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 142 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 50.0000 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 A 137 ASN A 188 ASN A 394 ASN A 422 ASN A 498 GLN A 607 GLN A 644 GLN A 655 HIS A 690 GLN A 703 ASN A 762 GLN A 787 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 992 GLN B 81 ASN B 115 GLN B 164 ASN B 188 ASN B 207 HIS B 239 GLN B 245 HIS B 422 ASN B 440 ASN B 498 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 755 GLN B 856 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 955 ASN B 992 GLN B1011 GLN C 30 ASN C 66 HIS C 239 GLN C 245 HIS C 314 GLN C 321 GLN C 422 ASN C 450 ASN C 498 GLN C 532 ASN C 641 ASN C 655 HIS C 804 GLN C 901 GLN C 907 ASN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 978 ASN C 992 GLN C1010 GLN C1071 GLN H 57 ASN H 101 GLN H 185 GLN I 39 GLN I 57 ASN I 185 GLN M 37 GLN M 90 GLN J 57 ASN ** N 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.211735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.177683 restraints weight = 60600.631| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.67 r_work: 0.3896 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35548 Z= 0.192 Angle : 0.882 18.004 48501 Z= 0.428 Chirality : 0.053 0.481 5670 Planarity : 0.006 0.071 6137 Dihedral : 9.222 96.131 6305 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.85 % Favored : 91.64 % Rotamer: Outliers : 5.36 % Allowed : 18.90 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.12), residues: 4280 helix: -0.23 (0.19), residues: 696 sheet: -1.02 (0.14), residues: 1306 loop : -2.67 (0.11), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 403 TYR 0.024 0.002 TYR N 32 PHE 0.022 0.002 PHE B 86 TRP 0.014 0.001 TRP I 36 HIS 0.008 0.002 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00429 (35426) covalent geometry : angle 0.83844 (48186) SS BOND : bond 0.00475 ( 51) SS BOND : angle 1.72586 ( 102) hydrogen bonds : bond 0.04513 ( 1142) hydrogen bonds : angle 6.01141 ( 3210) link_BETA1-4 : bond 0.01147 ( 23) link_BETA1-4 : angle 2.55099 ( 69) link_NAG-ASN : bond 0.00695 ( 48) link_NAG-ASN : angle 4.66940 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 362 time to evaluate : 1.259 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: A 572 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7315 (p) REVERT: B 158 ARG cc_start: 0.6105 (tpt-90) cc_final: 0.5854 (tpt-90) REVERT: B 160 TYR cc_start: 0.3903 (p90) cc_final: 0.3153 (p90) REVERT: B 270 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7587 (mt) REVERT: B 518 LEU cc_start: 0.2959 (OUTLIER) cc_final: 0.1640 (tt) REVERT: B 529 LYS cc_start: 0.5813 (OUTLIER) cc_final: 0.5486 (mmtm) REVERT: B 676 THR cc_start: 0.6026 (OUTLIER) cc_final: 0.5744 (m) REVERT: C 202 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7773 (mppt) REVERT: C 241 LEU cc_start: 0.7355 (mp) cc_final: 0.7095 (mt) REVERT: C 703 ASN cc_start: 0.7434 (t0) cc_final: 0.6943 (t0) REVERT: C 814 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7045 (mtpt) REVERT: C 856 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.6811 (p0) REVERT: C 1094 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7431 (m) REVERT: C 1138 TYR cc_start: 0.6741 (t80) cc_final: 0.6532 (t80) REVERT: H 76 LYS cc_start: 0.5105 (tttm) cc_final: 0.4440 (pttt) REVERT: H 207 THR cc_start: 0.2371 (OUTLIER) cc_final: 0.2045 (p) REVERT: K 4 MET cc_start: 0.2857 (OUTLIER) cc_final: 0.2358 (pmm) REVERT: I 83 MET cc_start: 0.0702 (mtm) cc_final: 0.0220 (ttp) REVERT: M 6 GLN cc_start: 0.4104 (mt0) cc_final: 0.3801 (tp40) REVERT: M 103 LYS cc_start: 0.4873 (ptpt) cc_final: 0.3843 (mmtp) REVERT: J 109 VAL cc_start: 0.5841 (m) cc_final: 0.5538 (m) outliers start: 203 outliers final: 100 residues processed: 540 average time/residue: 0.1848 time to fit residues: 170.7105 Evaluate side-chains 379 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 269 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 TYR Chi-restraints excluded: chain K residue 116 PHE Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 116 PHE Chi-restraints excluded: chain N residue 202 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 427 optimal weight: 10.0000 chunk 344 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 407 optimal weight: 50.0000 chunk 66 optimal weight: 2.9990 chunk 224 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 390 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 493 GLN A 658 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 955 ASN B1011 GLN B1054 GLN B1071 GLN C 66 HIS C 125 ASN C 207 HIS C 493 GLN C 907 ASN C1088 HIS H 185 GLN K 24 GLN K 100 GLN K 160 GLN I 39 GLN I 82 GLN I 185 GLN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN M 137 ASN J 82 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.202168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.165919 restraints weight = 59528.566| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.62 r_work: 0.3673 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 35548 Z= 0.277 Angle : 0.906 15.578 48501 Z= 0.443 Chirality : 0.055 0.480 5670 Planarity : 0.006 0.091 6137 Dihedral : 8.069 59.997 6188 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.86 % Favored : 90.86 % Rotamer: Outliers : 5.58 % Allowed : 19.71 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.20 (0.12), residues: 4280 helix: -0.08 (0.19), residues: 695 sheet: -0.91 (0.14), residues: 1365 loop : -2.32 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 190 TYR 0.028 0.002 TYR C 453 PHE 0.029 0.003 PHE I 180 TRP 0.040 0.002 TRP M 148 HIS 0.038 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00657 (35426) covalent geometry : angle 0.86768 (48186) SS BOND : bond 0.00901 ( 51) SS BOND : angle 2.18339 ( 102) hydrogen bonds : bond 0.05398 ( 1142) hydrogen bonds : angle 5.86257 ( 3210) link_BETA1-4 : bond 0.00870 ( 23) link_BETA1-4 : angle 3.05424 ( 69) link_NAG-ASN : bond 0.00623 ( 48) link_NAG-ASN : angle 4.07249 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 283 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 TYR cc_start: 0.8951 (m-80) cc_final: 0.8746 (m-80) REVERT: A 1142 GLN cc_start: 0.6964 (tp40) cc_final: 0.6761 (mm-40) REVERT: B 100 ILE cc_start: 0.7306 (mm) cc_final: 0.7071 (mm) REVERT: B 533 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7290 (tp) REVERT: B 722 VAL cc_start: 0.9341 (OUTLIER) cc_final: 0.9051 (t) REVERT: C 242 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6417 (mp) REVERT: C 335 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5743 (pt) REVERT: C 518 LEU cc_start: 0.2962 (OUTLIER) cc_final: 0.2645 (mt) REVERT: C 675 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6938 (mm-40) REVERT: C 814 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7346 (mtpt) REVERT: H 76 LYS cc_start: 0.5539 (tttm) cc_final: 0.4709 (mtmt) REVERT: H 207 THR cc_start: 0.2376 (OUTLIER) cc_final: 0.2030 (p) REVERT: K 4 MET cc_start: 0.3542 (OUTLIER) cc_final: 0.2136 (tpt) REVERT: I 72 ARG cc_start: 0.2919 (ptm160) cc_final: 0.2603 (ptm160) REVERT: I 81 LEU cc_start: 0.0368 (OUTLIER) cc_final: 0.0040 (tt) REVERT: I 83 MET cc_start: 0.0741 (mtm) cc_final: -0.0169 (ttp) REVERT: I 105 MET cc_start: 0.2698 (mpp) cc_final: 0.2472 (mpp) REVERT: M 6 GLN cc_start: 0.3715 (mt0) cc_final: 0.3488 (tp40) REVERT: M 100 GLN cc_start: 0.2441 (OUTLIER) cc_final: 0.0430 (tp-100) REVERT: M 179 LEU cc_start: 0.0104 (mt) cc_final: -0.0242 (tp) REVERT: J 130 THR cc_start: 0.2326 (OUTLIER) cc_final: 0.1942 (m) REVERT: J 178 HIS cc_start: 0.3173 (OUTLIER) cc_final: 0.2786 (m170) outliers start: 211 outliers final: 108 residues processed: 473 average time/residue: 0.1935 time to fit residues: 156.3106 Evaluate side-chains 323 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 202 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 178 HIS Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain N residue 85 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 12 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 249 optimal weight: 10.0000 chunk 379 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 235 optimal weight: 30.0000 chunk 354 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 481 ASN A 935 GLN A1113 GLN B 30 ASN B 125 ASN B 134 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 493 GLN B 955 ASN B1002 GLN C 87 ASN C 542 ASN C 607 GLN C 762 GLN C1002 GLN C1005 GLN C1010 GLN C1106 GLN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN M 100 GLN M 160 GLN J 107 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.199713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164864 restraints weight = 58294.550| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.47 r_work: 0.3619 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 35548 Z= 0.252 Angle : 0.812 14.712 48501 Z= 0.394 Chirality : 0.052 0.465 5670 Planarity : 0.006 0.065 6137 Dihedral : 7.673 59.784 6165 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.85 % Favored : 91.87 % Rotamer: Outliers : 5.15 % Allowed : 20.64 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.95 (0.12), residues: 4280 helix: 0.25 (0.19), residues: 702 sheet: -0.76 (0.14), residues: 1345 loop : -2.19 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 214 TYR 0.035 0.002 TYR B 369 PHE 0.021 0.002 PHE C1121 TRP 0.019 0.002 TRP M 148 HIS 0.016 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00612 (35426) covalent geometry : angle 0.77684 (48186) SS BOND : bond 0.00504 ( 51) SS BOND : angle 1.88458 ( 102) hydrogen bonds : bond 0.04886 ( 1142) hydrogen bonds : angle 5.60632 ( 3210) link_BETA1-4 : bond 0.00616 ( 23) link_BETA1-4 : angle 2.61486 ( 69) link_NAG-ASN : bond 0.00490 ( 48) link_NAG-ASN : angle 3.76850 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 225 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5919 (m-30) REVERT: A 161 SER cc_start: 0.6679 (OUTLIER) cc_final: 0.6021 (p) REVERT: A 313 TYR cc_start: 0.9115 (m-80) cc_final: 0.8869 (m-80) REVERT: A 584 ILE cc_start: 0.8193 (mm) cc_final: 0.7875 (mm) REVERT: A 726 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9007 (mp) REVERT: A 735 SER cc_start: 0.8756 (t) cc_final: 0.8531 (p) REVERT: A 1142 GLN cc_start: 0.7012 (tp40) cc_final: 0.6785 (mm-40) REVERT: B 162 SER cc_start: 0.5565 (OUTLIER) cc_final: 0.4854 (p) REVERT: B 533 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7315 (tp) REVERT: B 576 VAL cc_start: 0.9398 (OUTLIER) cc_final: 0.9015 (t) REVERT: B 722 VAL cc_start: 0.9412 (OUTLIER) cc_final: 0.9090 (t) REVERT: B 780 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: C 52 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 378 LYS cc_start: 0.4573 (tptt) cc_final: 0.4335 (tptm) REVERT: C 1086 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8101 (mtmm) REVERT: C 1132 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8758 (mt) REVERT: H 76 LYS cc_start: 0.5463 (tttm) cc_final: 0.4746 (mtmt) REVERT: H 207 THR cc_start: 0.2765 (OUTLIER) cc_final: 0.2247 (p) REVERT: K 4 MET cc_start: 0.3950 (OUTLIER) cc_final: 0.3328 (pmm) REVERT: M 6 GLN cc_start: 0.3795 (mt0) cc_final: 0.3446 (tp40) REVERT: M 39 LYS cc_start: 0.2343 (tppt) cc_final: 0.1906 (mmtt) REVERT: J 130 THR cc_start: 0.2855 (OUTLIER) cc_final: 0.2613 (m) REVERT: J 178 HIS cc_start: 0.3236 (OUTLIER) cc_final: 0.2654 (m170) outliers start: 195 outliers final: 116 residues processed: 402 average time/residue: 0.1930 time to fit residues: 132.7609 Evaluate side-chains 319 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 189 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE 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 1086 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 178 HIS Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 215 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 222 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 324 optimal weight: 30.0000 chunk 125 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 336 optimal weight: 30.0000 chunk 406 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 207 HIS B 955 ASN C1005 GLN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.200518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.166182 restraints weight = 58266.743| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.46 r_work: 0.3701 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35548 Z= 0.165 Angle : 0.730 16.431 48501 Z= 0.350 Chirality : 0.048 0.475 5670 Planarity : 0.005 0.058 6137 Dihedral : 7.270 59.449 6161 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.73 % Favored : 92.03 % Rotamer: Outliers : 4.20 % Allowed : 21.96 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.64 (0.12), residues: 4280 helix: 0.71 (0.20), residues: 692 sheet: -0.56 (0.14), residues: 1369 loop : -2.07 (0.12), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.023 0.001 TYR K 91 PHE 0.018 0.002 PHE A 400 TRP 0.012 0.001 TRP H 117 HIS 0.006 0.001 HIS M 189 Details of bonding type rmsd covalent geometry : bond 0.00391 (35426) covalent geometry : angle 0.69361 (48186) SS BOND : bond 0.00657 ( 51) SS BOND : angle 1.42321 ( 102) hydrogen bonds : bond 0.04115 ( 1142) hydrogen bonds : angle 5.35000 ( 3210) link_BETA1-4 : bond 0.00877 ( 23) link_BETA1-4 : angle 2.34645 ( 69) link_NAG-ASN : bond 0.00442 ( 48) link_NAG-ASN : angle 3.81666 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 216 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 SER cc_start: 0.6826 (OUTLIER) cc_final: 0.6123 (p) REVERT: A 584 ILE cc_start: 0.8234 (mm) cc_final: 0.7997 (mm) REVERT: A 726 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8930 (mp) REVERT: A 735 SER cc_start: 0.8879 (t) cc_final: 0.8613 (p) REVERT: A 1144 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6736 (tp30) REVERT: B 319 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7872 (ttm-80) REVERT: B 342 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.5841 (m-80) REVERT: B 533 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7553 (tp) REVERT: B 576 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9061 (t) REVERT: C 96 GLU cc_start: 0.5164 (OUTLIER) cc_final: 0.4957 (pm20) REVERT: C 1132 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8792 (mt) REVERT: H 207 THR cc_start: 0.2589 (OUTLIER) cc_final: 0.2085 (p) REVERT: K 4 MET cc_start: 0.3777 (OUTLIER) cc_final: 0.3454 (pmm) REVERT: I 83 MET cc_start: 0.0513 (mtm) cc_final: -0.1105 (tmm) REVERT: M 6 GLN cc_start: 0.3981 (mt0) cc_final: 0.3650 (tp40) REVERT: M 39 LYS cc_start: 0.2518 (tppt) cc_final: 0.1982 (mmtt) REVERT: J 130 THR cc_start: 0.2647 (OUTLIER) cc_final: 0.2441 (m) REVERT: J 178 HIS cc_start: 0.3299 (OUTLIER) cc_final: 0.2613 (m170) REVERT: J 215 LYS cc_start: 0.2531 (OUTLIER) cc_final: 0.0807 (mmtp) REVERT: N 42 LYS cc_start: 0.1361 (tmtt) cc_final: 0.0879 (ptmt) outliers start: 159 outliers final: 106 residues processed: 361 average time/residue: 0.1934 time to fit residues: 119.3413 Evaluate side-chains 312 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 193 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 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 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 178 HIS Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain N residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 178 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 340 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN C1005 GLN H 185 GLN K 189 HIS M 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.199942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.166327 restraints weight = 57937.611| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.43 r_work: 0.3715 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35548 Z= 0.173 Angle : 0.725 17.604 48501 Z= 0.347 Chirality : 0.048 0.473 5670 Planarity : 0.005 0.058 6137 Dihedral : 7.105 59.946 6159 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.52 % Favored : 92.29 % Rotamer: Outliers : 4.55 % Allowed : 21.93 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.53 (0.12), residues: 4280 helix: 0.80 (0.20), residues: 697 sheet: -0.47 (0.14), residues: 1349 loop : -2.01 (0.12), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.021 0.001 TYR K 91 PHE 0.017 0.002 PHE A 486 TRP 0.013 0.001 TRP H 117 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00414 (35426) covalent geometry : angle 0.68759 (48186) SS BOND : bond 0.00435 ( 51) SS BOND : angle 1.35500 ( 102) hydrogen bonds : bond 0.04130 ( 1142) hydrogen bonds : angle 5.27912 ( 3210) link_BETA1-4 : bond 0.00564 ( 23) link_BETA1-4 : angle 2.27027 ( 69) link_NAG-ASN : bond 0.00490 ( 48) link_NAG-ASN : angle 3.87164 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 202 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.6798 (m-70) REVERT: A 111 ASP cc_start: 0.5862 (OUTLIER) cc_final: 0.5572 (m-30) REVERT: A 161 SER cc_start: 0.6908 (OUTLIER) cc_final: 0.6262 (p) REVERT: A 584 ILE cc_start: 0.8321 (mm) cc_final: 0.8047 (mm) REVERT: A 726 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8930 (mp) REVERT: A 1144 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6909 (tp30) REVERT: B 342 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6018 (m-80) REVERT: B 533 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7599 (tp) REVERT: B 780 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: B 1141 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8577 (mt) REVERT: C 242 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6265 (mp) REVERT: C 332 ILE cc_start: 0.4999 (OUTLIER) cc_final: 0.4757 (mt) REVERT: C 574 ASP cc_start: 0.8897 (p0) cc_final: 0.8674 (p0) REVERT: C 1132 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8807 (mt) REVERT: H 76 LYS cc_start: 0.5340 (tttm) cc_final: 0.4774 (mtmt) REVERT: H 99 ASP cc_start: 0.4095 (OUTLIER) cc_final: 0.3775 (m-30) REVERT: H 207 THR cc_start: 0.2265 (OUTLIER) cc_final: 0.1753 (p) REVERT: K 4 MET cc_start: 0.3837 (OUTLIER) cc_final: 0.3539 (pmm) REVERT: I 83 MET cc_start: 0.0390 (mtm) cc_final: -0.1237 (tmm) REVERT: M 6 GLN cc_start: 0.4048 (mt0) cc_final: 0.3739 (tp40) REVERT: M 208 SER cc_start: 0.5335 (OUTLIER) cc_final: 0.4959 (p) REVERT: J 130 THR cc_start: 0.2651 (OUTLIER) cc_final: 0.2430 (m) REVERT: J 178 HIS cc_start: 0.3290 (OUTLIER) cc_final: 0.2516 (m170) REVERT: N 50 ASP cc_start: 0.4912 (OUTLIER) cc_final: 0.3480 (m-30) outliers start: 172 outliers final: 118 residues processed: 356 average time/residue: 0.1927 time to fit residues: 117.9225 Evaluate side-chains 321 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 184 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 859 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 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 178 HIS Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain N residue 50 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 187 optimal weight: 0.9980 chunk 412 optimal weight: 0.0770 chunk 236 optimal weight: 8.9990 chunk 245 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 280 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 298 optimal weight: 4.9990 chunk 341 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 207 HIS B 354 ASN B 422 ASN C1005 GLN I 107 GLN M 37 GLN M 100 GLN J 185 GLN ** J 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** 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 = 0.4469 r_free = 0.4469 target = 0.202517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.166354 restraints weight = 58256.759| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.58 r_work: 0.3699 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35548 Z= 0.107 Angle : 0.653 16.421 48501 Z= 0.313 Chirality : 0.046 0.442 5670 Planarity : 0.004 0.055 6137 Dihedral : 6.468 56.833 6158 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.50 % Favored : 93.34 % Rotamer: Outliers : 2.64 % Allowed : 23.86 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 4280 helix: 1.30 (0.21), residues: 684 sheet: -0.16 (0.14), residues: 1313 loop : -1.88 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.016 0.001 TYR M 86 PHE 0.030 0.001 PHE A 643 TRP 0.009 0.001 TRP H 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00234 (35426) covalent geometry : angle 0.62185 (48186) SS BOND : bond 0.00485 ( 51) SS BOND : angle 1.23029 ( 102) hydrogen bonds : bond 0.03205 ( 1142) hydrogen bonds : angle 4.93905 ( 3210) link_BETA1-4 : bond 0.00570 ( 23) link_BETA1-4 : angle 1.98515 ( 69) link_NAG-ASN : bond 0.00540 ( 48) link_NAG-ASN : angle 3.37298 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 216 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6605 (m-70) REVERT: A 111 ASP cc_start: 0.6007 (OUTLIER) cc_final: 0.5707 (m-30) REVERT: A 161 SER cc_start: 0.6734 (OUTLIER) cc_final: 0.5931 (p) REVERT: A 584 ILE cc_start: 0.8283 (mm) cc_final: 0.8061 (mm) REVERT: B 319 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7521 (ttt90) REVERT: B 533 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7585 (tp) REVERT: C 574 ASP cc_start: 0.8667 (p0) cc_final: 0.8424 (p0) REVERT: C 1132 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8702 (mt) REVERT: H 76 LYS cc_start: 0.5302 (tttm) cc_final: 0.4806 (mtmt) REVERT: K 4 MET cc_start: 0.3826 (OUTLIER) cc_final: 0.3554 (pmm) REVERT: M 6 GLN cc_start: 0.4381 (mt0) cc_final: 0.3922 (tp40) REVERT: M 208 SER cc_start: 0.5816 (OUTLIER) cc_final: 0.5381 (p) REVERT: N 50 ASP cc_start: 0.4739 (OUTLIER) cc_final: 0.3339 (m-30) outliers start: 100 outliers final: 64 residues processed: 310 average time/residue: 0.2078 time to fit residues: 108.1055 Evaluate side-chains 256 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 184 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain N residue 50 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 244 optimal weight: 6.9990 chunk 230 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 43 optimal weight: 30.0000 chunk 67 optimal weight: 4.9990 chunk 302 optimal weight: 20.0000 chunk 303 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN M 100 GLN ** J 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.199835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.166060 restraints weight = 57791.967| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.43 r_work: 0.3670 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.7586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35548 Z= 0.183 Angle : 0.711 16.092 48501 Z= 0.341 Chirality : 0.048 0.471 5670 Planarity : 0.005 0.057 6137 Dihedral : 6.758 59.635 6158 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.64 % Favored : 92.20 % Rotamer: Outliers : 3.30 % Allowed : 23.57 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.23 (0.13), residues: 4280 helix: 1.17 (0.20), residues: 692 sheet: -0.16 (0.14), residues: 1336 loop : -1.94 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.020 0.001 TYR B1067 PHE 0.026 0.002 PHE A 643 TRP 0.015 0.001 TRP H 117 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00446 (35426) covalent geometry : angle 0.67928 (48186) SS BOND : bond 0.00536 ( 51) SS BOND : angle 1.40603 ( 102) hydrogen bonds : bond 0.04108 ( 1142) hydrogen bonds : angle 5.08582 ( 3210) link_BETA1-4 : bond 0.00593 ( 23) link_BETA1-4 : angle 2.18270 ( 69) link_NAG-ASN : bond 0.00439 ( 48) link_NAG-ASN : angle 3.51450 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 191 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6780 (m-70) REVERT: A 111 ASP cc_start: 0.5875 (OUTLIER) cc_final: 0.5671 (m-30) REVERT: B 319 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7578 (ttt90) REVERT: B 533 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7749 (tp) REVERT: B 780 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: C 242 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6313 (mp) REVERT: C 574 ASP cc_start: 0.8941 (p0) cc_final: 0.8722 (p0) REVERT: C 1132 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8800 (mt) REVERT: H 76 LYS cc_start: 0.5330 (tttm) cc_final: 0.4837 (mtmt) REVERT: H 124 THR cc_start: 0.5488 (OUTLIER) cc_final: 0.4878 (p) REVERT: K 4 MET cc_start: 0.3810 (OUTLIER) cc_final: 0.3543 (pmm) REVERT: I 83 MET cc_start: 0.1025 (mtm) cc_final: -0.1218 (tmm) REVERT: M 6 GLN cc_start: 0.4369 (mt0) cc_final: 0.3833 (tp40) REVERT: M 208 SER cc_start: 0.5691 (OUTLIER) cc_final: 0.5252 (p) REVERT: J 178 HIS cc_start: 0.3159 (OUTLIER) cc_final: 0.2395 (m170) REVERT: N 50 ASP cc_start: 0.4902 (OUTLIER) cc_final: 0.3576 (m-30) outliers start: 125 outliers final: 92 residues processed: 300 average time/residue: 0.1971 time to fit residues: 100.6452 Evaluate side-chains 288 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 185 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 178 HIS Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain N residue 50 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 127 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 316 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 269 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 201 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN C1005 GLN M 100 GLN ** J 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.201587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.167120 restraints weight = 57584.073| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.43 r_work: 0.3689 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.7668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35548 Z= 0.112 Angle : 0.657 16.464 48501 Z= 0.315 Chirality : 0.046 0.456 5670 Planarity : 0.004 0.054 6137 Dihedral : 6.446 56.777 6156 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.82 % Favored : 93.06 % Rotamer: Outliers : 2.93 % Allowed : 23.78 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.07 (0.13), residues: 4280 helix: 1.40 (0.21), residues: 686 sheet: -0.07 (0.14), residues: 1326 loop : -1.85 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.025 0.001 TYR C 453 PHE 0.026 0.001 PHE A 643 TRP 0.010 0.001 TRP H 117 HIS 0.009 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00252 (35426) covalent geometry : angle 0.62824 (48186) SS BOND : bond 0.00392 ( 51) SS BOND : angle 1.13284 ( 102) hydrogen bonds : bond 0.03464 ( 1142) hydrogen bonds : angle 4.93054 ( 3210) link_BETA1-4 : bond 0.00533 ( 23) link_BETA1-4 : angle 1.97249 ( 69) link_NAG-ASN : bond 0.00513 ( 48) link_NAG-ASN : angle 3.27182 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 191 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7116 (OUTLIER) cc_final: 0.6656 (m-70) REVERT: A 111 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5770 (m-30) REVERT: B 319 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7555 (ttt90) REVERT: C 190 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7943 (mmt90) REVERT: C 242 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6189 (mp) REVERT: C 332 ILE cc_start: 0.4775 (OUTLIER) cc_final: 0.4506 (mt) REVERT: C 574 ASP cc_start: 0.8898 (p0) cc_final: 0.8646 (p0) REVERT: C 1132 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8769 (mt) REVERT: H 76 LYS cc_start: 0.5379 (tttm) cc_final: 0.4897 (mtmt) REVERT: H 124 THR cc_start: 0.5409 (OUTLIER) cc_final: 0.4804 (p) REVERT: K 4 MET cc_start: 0.3818 (OUTLIER) cc_final: 0.3550 (pmm) REVERT: I 83 MET cc_start: 0.0824 (mtm) cc_final: -0.1395 (tmm) REVERT: M 6 GLN cc_start: 0.4318 (mt0) cc_final: 0.3746 (tp40) REVERT: M 100 GLN cc_start: 0.1627 (OUTLIER) cc_final: -0.0214 (mm-40) REVERT: M 208 SER cc_start: 0.5748 (OUTLIER) cc_final: 0.5328 (p) REVERT: J 178 HIS cc_start: 0.3160 (OUTLIER) cc_final: 0.2408 (m170) REVERT: J 228 LYS cc_start: 0.0399 (mttp) cc_final: -0.1518 (tppt) REVERT: N 42 LYS cc_start: 0.1068 (tmtt) cc_final: 0.0524 (ptmt) REVERT: N 50 ASP cc_start: 0.4755 (OUTLIER) cc_final: 0.3277 (m-30) outliers start: 111 outliers final: 80 residues processed: 294 average time/residue: 0.2010 time to fit residues: 100.2482 Evaluate side-chains 277 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 185 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 178 HIS Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain N residue 50 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 315 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 397 optimal weight: 20.0000 chunk 375 optimal weight: 9.9990 chunk 380 optimal weight: 40.0000 chunk 329 optimal weight: 7.9990 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 137 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C1005 GLN ** J 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.201214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.165892 restraints weight = 58128.189| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.53 r_work: 0.3634 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.7683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 35548 Z= 0.191 Angle : 0.799 59.199 48501 Z= 0.422 Chirality : 0.049 0.709 5670 Planarity : 0.005 0.121 6137 Dihedral : 6.420 56.969 6154 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.03 % Favored : 92.85 % Rotamer: Outliers : 2.83 % Allowed : 23.78 % Favored : 73.39 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.08 (0.13), residues: 4280 helix: 1.35 (0.21), residues: 687 sheet: -0.06 (0.14), residues: 1326 loop : -1.85 (0.12), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.022 0.001 TYR C 495 PHE 0.025 0.002 PHE A 643 TRP 0.009 0.001 TRP H 117 HIS 0.007 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00447 (35426) covalent geometry : angle 0.77393 (48186) SS BOND : bond 0.00489 ( 51) SS BOND : angle 1.40348 ( 102) hydrogen bonds : bond 0.03634 ( 1142) hydrogen bonds : angle 4.92870 ( 3210) link_BETA1-4 : bond 0.00481 ( 23) link_BETA1-4 : angle 2.01821 ( 69) link_NAG-ASN : bond 0.00668 ( 48) link_NAG-ASN : angle 3.32565 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 186 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6660 (m-70) REVERT: A 111 ASP cc_start: 0.5798 (OUTLIER) cc_final: 0.5533 (m-30) REVERT: B 319 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7547 (ttt90) REVERT: C 190 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7785 (mmt90) REVERT: C 242 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6159 (mp) REVERT: C 332 ILE cc_start: 0.4761 (OUTLIER) cc_final: 0.4492 (mt) REVERT: C 574 ASP cc_start: 0.8675 (p0) cc_final: 0.8420 (p0) REVERT: C 1132 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8753 (mt) REVERT: H 76 LYS cc_start: 0.5375 (tttm) cc_final: 0.4903 (mtmt) REVERT: H 124 THR cc_start: 0.5346 (OUTLIER) cc_final: 0.4767 (p) REVERT: K 4 MET cc_start: 0.3851 (OUTLIER) cc_final: 0.3595 (pmm) REVERT: I 83 MET cc_start: 0.0747 (mtm) cc_final: -0.1440 (tmm) REVERT: M 6 GLN cc_start: 0.4265 (mt0) cc_final: 0.3719 (tp40) REVERT: M 208 SER cc_start: 0.5787 (OUTLIER) cc_final: 0.5373 (p) REVERT: J 178 HIS cc_start: 0.3075 (OUTLIER) cc_final: 0.2328 (m170) REVERT: J 228 LYS cc_start: 0.0414 (mttp) cc_final: -0.1522 (tppt) REVERT: N 42 LYS cc_start: 0.0897 (tmtt) cc_final: 0.0424 (ptmt) REVERT: N 50 ASP cc_start: 0.4702 (OUTLIER) cc_final: 0.3246 (m-30) outliers start: 107 outliers final: 92 residues processed: 284 average time/residue: 0.2032 time to fit residues: 96.8865 Evaluate side-chains 288 residues out of total 3784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 185 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 178 HIS Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain N residue 50 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 424 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 227 optimal weight: 20.0000 chunk 279 optimal weight: 1.9990 chunk 327 optimal weight: 20.0000 chunk 416 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN H 101 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.200990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164625 restraints weight = 57667.834| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.53 r_work: 0.3675 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.7678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 35548 Z= 0.191 Angle : 0.799 59.199 48501 Z= 0.422 Chirality : 0.049 0.709 5670 Planarity : 0.005 0.121 6137 Dihedral : 6.420 56.969 6154 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.03 % Favored : 92.85 % Rotamer: Outliers : 2.72 % Allowed : 23.81 % Favored : 73.47 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.08 (0.13), residues: 4280 helix: 1.35 (0.21), residues: 687 sheet: -0.06 (0.14), residues: 1326 loop : -1.85 (0.12), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.022 0.001 TYR C 495 PHE 0.025 0.002 PHE A 643 TRP 0.009 0.001 TRP H 117 HIS 0.007 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00447 (35426) covalent geometry : angle 0.77393 (48186) SS BOND : bond 0.00489 ( 51) SS BOND : angle 1.40348 ( 102) hydrogen bonds : bond 0.03634 ( 1142) hydrogen bonds : angle 4.92870 ( 3210) link_BETA1-4 : bond 0.00481 ( 23) link_BETA1-4 : angle 2.01821 ( 69) link_NAG-ASN : bond 0.00668 ( 48) link_NAG-ASN : angle 3.32565 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8388.42 seconds wall clock time: 144 minutes 36.37 seconds (8676.37 seconds total)