Starting phenix.real_space_refine on Fri Mar 6 20:18:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7czs_30515/03_2026/7czs_30515.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czs_30515/03_2026/7czs_30515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7czs_30515/03_2026/7czs_30515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czs_30515/03_2026/7czs_30515.map" model { file = "/net/cci-nas-00/data/ceres_data/7czs_30515/03_2026/7czs_30515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czs_30515/03_2026/7czs_30515.cif" } resolution = 3.6 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 141 5.16 5 C 21759 2.51 5 N 5619 2.21 5 O 6802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34321 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: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "K" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "I" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "M" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "J" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "N" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} 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: 8.32, per 1000 atoms: 0.24 Number of scatterers: 34321 At special positions: 0 Unit cell: (146.745, 175.007, 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 141 16.00 O 6802 8.00 N 5619 7.00 C 21759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, 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=2.52 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.29 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 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.29 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=2.09 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=2.29 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 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 3.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8030 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 76 sheets defined 18.4% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 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: 3.686A 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: 3.771A 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: 4.176A 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: 3.557A 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: 3.646A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.575A 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: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.680A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A 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: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.686A 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: 3.738A 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: 3.963A 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: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A 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: 4.012A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.706A 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: 4.118A 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: 4.256A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.623A 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: 3.584A 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: 3.717A 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: 3.603A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.713A 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: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.537A 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 28 through 32 removed outlier: 4.237A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.238A pdb=" N ASN I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 191 No H-bonds generated for 'chain 'I' and resid 189 through 191' Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing helix chain 'J' and resid 28 through 32 removed outlier: 4.237A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 191 No H-bonds generated for 'chain 'J' and resid 189 through 191' 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: 8.061A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A 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: 3.683A 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: 4.437A 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: 3.571A 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: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A 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: 4.589A 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: 4.045A 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: 3.547A 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: 4.848A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A 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: 3.543A 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: 4.784A 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: 6.604A 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: 5.734A 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: 6.604A 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: 6.610A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.375A 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: 7.028A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.163A 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: 4.267A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.614A 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: 3.517A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.821A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.188A 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: 7.420A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.544A 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: 3.543A 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: 4.783A 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: 6.444A 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: 8.613A 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: 6.540A 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: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.166A 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: 6.540A 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: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A 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: 3.799A 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: 3.558A 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: 5.759A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.706A 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: 3.543A 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: 5.863A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.783A 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: 6.280A 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: 6.841A 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: 5.819A 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: 6.841A 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 45 through 51 removed outlier: 6.530A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA H 139 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 186 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 141 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 184 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 143 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER H 182 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 145 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 180 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA H 139 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 186 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 141 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 184 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 143 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER H 182 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 145 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 180 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 152 through 156 Processing sheet with id=AG1, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.527A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG3, first strand: chain 'K' and resid 114 through 118 Processing sheet with id=AG4, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG5, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AG6, first strand: chain 'I' and resid 45 through 51 removed outlier: 6.530A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR I 33 " --> pdb=" O GLU I 98 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 123 through 126 removed outlier: 5.010A pdb=" N ALA I 139 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 186 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY I 141 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 184 " --> pdb=" O GLY I 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 143 " --> pdb=" O SER I 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 182 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS I 145 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU I 180 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 123 through 126 removed outlier: 5.010A pdb=" N ALA I 139 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 186 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY I 141 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 184 " --> pdb=" O GLY I 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 143 " --> pdb=" O SER I 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 182 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS I 145 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU I 180 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 152 through 156 Processing sheet with id=AH1, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.526A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AH3, first strand: chain 'M' and resid 114 through 118 Processing sheet with id=AH4, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AH5, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AH6, first strand: chain 'J' and resid 45 through 51 removed outlier: 6.531A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR J 33 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA J 139 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL J 186 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 141 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL J 184 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 143 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 182 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 145 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 180 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA J 139 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL J 186 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 141 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL J 184 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 143 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 182 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 145 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 180 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 152 through 156 Processing sheet with id=AI1, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.526A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AI3, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AI4, first strand: chain 'N' and resid 153 through 154 1193 hydrogen bonds defined for protein. 3183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.47 Time building geometry restraints manager: 4.07 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: 5730 1.32 - 1.45: 10423 1.45 - 1.58: 18739 1.58 - 1.72: 3 1.72 - 1.85: 174 Bond restraints: 35069 Sorted by residual: bond pdb=" CA HIS B 49 " pdb=" C HIS B 49 " ideal model delta sigma weight residual 1.520 1.405 0.115 1.22e-02 6.72e+03 8.96e+01 bond pdb=" CA GLN C 239 " pdb=" C GLN C 239 " ideal model delta sigma weight residual 1.525 1.420 0.105 1.11e-02 8.12e+03 8.92e+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 8.16e+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 7.38e+01 bond pdb=" CA TYR B 204 " pdb=" C TYR B 204 " ideal model delta sigma weight residual 1.523 1.422 0.101 1.18e-02 7.18e+03 7.29e+01 ... (remaining 35064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 45449 2.70 - 5.41: 1874 5.41 - 8.11: 289 8.11 - 10.81: 60 10.81 - 13.52: 28 Bond angle restraints: 47700 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 113.80 103.50 10.30 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 117.82 125.26 -7.44 7.80e-01 1.64e+00 9.09e+01 angle pdb=" CA GLU C 224 " pdb=" C GLU C 224 " pdb=" O GLU C 224 " ideal model delta sigma weight residual 120.19 112.57 7.62 8.40e-01 1.42e+00 8.23e+01 angle pdb=" CA ASN B 188 " pdb=" CB ASN B 188 " pdb=" CG ASN B 188 " ideal model delta sigma weight residual 112.60 103.62 8.98 1.00e+00 1.00e+00 8.06e+01 angle pdb=" CA PHE C 238 " pdb=" CB PHE C 238 " pdb=" CG PHE C 238 " ideal model delta sigma weight residual 113.80 122.40 -8.60 1.00e+00 1.00e+00 7.40e+01 ... (remaining 47695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 18843 17.91 - 35.83: 2124 35.83 - 53.74: 615 53.74 - 71.66: 206 71.66 - 89.57: 65 Dihedral angle restraints: 21853 sinusoidal: 9354 harmonic: 12499 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 21.07 71.93 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 156.46 -63.46 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 156.45 -63.45 1 1.00e+01 1.00e-02 5.31e+01 ... (remaining 21850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5582 0.328 - 0.656: 33 0.656 - 0.984: 8 0.984 - 1.312: 2 1.312 - 1.640: 3 Chirality restraints: 5628 Sorted by residual: 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 -0.77 -1.63 2.00e-02 2.50e+03 6.62e+03 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 -3.45 1.05 2.00e-02 2.50e+03 2.73e+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 ... (remaining 5625 not shown) Planarity restraints: 6110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 282 " 0.243 2.00e-02 2.50e+03 3.37e-01 1.42e+03 pdb=" CG ASN B 282 " -0.115 2.00e-02 2.50e+03 pdb=" OD1 ASN B 282 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 282 " -0.561 2.00e-02 2.50e+03 pdb=" C1 NAG B1405 " 0.424 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG P 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.189 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 ... (remaining 6107 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 431 2.51 - 3.11: 25827 3.11 - 3.71: 49612 3.71 - 4.30: 74169 4.30 - 4.90: 122995 Nonbonded interactions: 273034 Sorted by model distance: nonbonded pdb=" O ARG C 273 " pdb=" OG1 THR C 274 " model vdw 1.914 3.040 nonbonded pdb=" O ALA C 522 " pdb=" OG1 THR C 523 " model vdw 1.923 3.040 nonbonded pdb=" O ASN A 334 " pdb=" ND2 ASN A 334 " model vdw 1.924 3.120 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.981 3.120 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.982 3.120 ... (remaining 273029 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.080 Process input model: 35.080 Find NCS groups from input model: 0.980 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 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 0.489 35190 Z= 0.725 Angle : 1.590 56.767 48013 Z= 0.856 Chirality : 0.091 1.640 5628 Planarity : 0.010 0.302 6062 Dihedral : 17.507 89.571 13673 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 35.65 Ramachandran Plot: Outliers : 4.08 % Allowed : 11.55 % Favored : 84.38 % Rotamer: Outliers : 12.67 % Allowed : 17.10 % Favored : 70.23 % 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: -4.03 (0.11), residues: 4244 helix: -2.26 (0.16), residues: 683 sheet: -1.74 (0.14), residues: 1215 loop : -3.46 (0.11), residues: 2346 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 0.009 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.01263 (35069) covalent geometry : angle 1.30113 (47700) SS BOND : bond 0.09849 ( 50) SS BOND : angle 11.36433 ( 100) hydrogen bonds : bond 0.21339 ( 1139) hydrogen bonds : angle 8.58059 ( 3183) link_BETA1-4 : bond 0.09999 ( 23) link_BETA1-4 : angle 11.29437 ( 69) link_NAG-ASN : bond 0.06537 ( 48) link_NAG-ASN : angle 11.46813 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 474 poor density : 573 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8324 (mm) cc_final: 0.8077 (mt) REVERT: A 203 ILE cc_start: 0.7006 (mt) cc_final: 0.6675 (mt) REVERT: A 231 ILE cc_start: 0.4068 (OUTLIER) cc_final: 0.3683 (mt) REVERT: A 438 SER cc_start: 0.1285 (OUTLIER) cc_final: 0.0154 (m) REVERT: A 537 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6707 (mtpp) REVERT: A 939 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.7382 (m) REVERT: A 998 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8379 (p) REVERT: B 114 THR cc_start: 0.2564 (OUTLIER) cc_final: 0.2359 (m) REVERT: B 214 ARG cc_start: 0.0733 (OUTLIER) cc_final: -0.0266 (ttm110) REVERT: B 459 SER cc_start: 0.4892 (OUTLIER) cc_final: 0.4589 (m) REVERT: B 517 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.4171 (pt) REVERT: B 540 ASN cc_start: 0.6890 (OUTLIER) cc_final: 0.6687 (t0) REVERT: B 588 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8330 (m) REVERT: B 591 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8126 (m) REVERT: B 697 MET cc_start: 0.7834 (ptm) cc_final: 0.7563 (ptp) REVERT: B 869 MET cc_start: 0.7766 (mtt) cc_final: 0.7517 (mtt) REVERT: B 917 TYR cc_start: 0.8367 (m-80) cc_final: 0.8108 (m-80) REVERT: C 214 ARG cc_start: -0.0598 (OUTLIER) cc_final: -0.1647 (mtt180) REVERT: C 305 SER cc_start: 0.7047 (OUTLIER) cc_final: 0.6756 (t) REVERT: C 517 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5523 (mp) REVERT: C 547 THR cc_start: 0.7539 (m) cc_final: 0.7111 (p) REVERT: C 699 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8439 (mt) REVERT: C 787 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: C 794 ILE cc_start: 0.7680 (mp) cc_final: 0.7438 (tt) REVERT: C 814 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.6208 (ptpt) REVERT: C 904 TYR cc_start: 0.8019 (m-10) cc_final: 0.7800 (m-10) REVERT: C 917 TYR cc_start: 0.8668 (m-80) cc_final: 0.8297 (m-80) REVERT: H 13 GLN cc_start: 0.5188 (OUTLIER) cc_final: 0.4885 (pt0) REVERT: H 33 TYR cc_start: 0.3049 (m-80) cc_final: 0.2177 (m-80) REVERT: H 158 SER cc_start: 0.1954 (OUTLIER) cc_final: 0.1662 (p) REVERT: I 140 LEU cc_start: 0.0697 (OUTLIER) cc_final: 0.0129 (mp) REVERT: I 158 SER cc_start: 0.2620 (OUTLIER) cc_final: 0.2311 (m) REVERT: I 199 ASN cc_start: 0.3497 (OUTLIER) cc_final: 0.2386 (t0) REVERT: M 63 SER cc_start: 0.4912 (OUTLIER) cc_final: 0.4663 (m) REVERT: J 63 VAL cc_start: 0.0504 (OUTLIER) cc_final: 0.0123 (m) REVERT: J 100 LEU cc_start: 0.2930 (OUTLIER) cc_final: 0.2701 (mt) REVERT: N 49 TYR cc_start: 0.3254 (OUTLIER) cc_final: 0.2851 (t80) REVERT: N 54 LEU cc_start: 0.1427 (OUTLIER) cc_final: 0.0635 (mp) REVERT: N 110 VAL cc_start: 0.4253 (t) cc_final: 0.3916 (m) outliers start: 474 outliers final: 83 residues processed: 969 average time/residue: 0.2160 time to fit residues: 340.4460 Evaluate side-chains 393 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 282 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 102 ARG 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 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 974 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 81 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 214 ARG 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 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 166 HIS Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 202 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 81 ASN A 134 GLN A 137 ASN A 188 ASN A 422 ASN A 450 ASN A 498 GLN A 644 GLN A 690 GLN A 764 ASN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 969 ASN A1101 HIS B 81 ASN B 115 GLN B 188 ASN B 239 GLN B 245 HIS B 422 ASN B 440 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 703 ASN B 901 GLN B 913 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 949 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 30 ASN C 81 ASN C 87 ASN C 115 GLN C 388 ASN C 422 ASN C 440 ASN C 493 GLN C 498 GLN C 544 ASN C 641 ASN C 655 HIS C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1010 GLN C1071 GLN C1101 HIS H 81 GLN K 90 GLN M 37 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.208586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.179541 restraints weight = 67948.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.175671 restraints weight = 116338.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.172092 restraints weight = 115856.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.171462 restraints weight = 119818.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.169867 restraints weight = 97186.434| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35190 Z= 0.180 Angle : 0.920 17.770 48013 Z= 0.442 Chirality : 0.055 0.798 5628 Planarity : 0.006 0.059 6062 Dihedral : 9.566 61.562 6292 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.34 % Favored : 91.05 % Rotamer: Outliers : 5.69 % Allowed : 19.67 % Favored : 74.64 % 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: -2.64 (0.12), residues: 4244 helix: -0.13 (0.19), residues: 693 sheet: -0.83 (0.14), residues: 1198 loop : -2.91 (0.11), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 454 TYR 0.030 0.002 TYR M 32 PHE 0.025 0.002 PHE C 133 TRP 0.023 0.002 TRP I 105 HIS 0.008 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00402 (35069) covalent geometry : angle 0.86851 (47700) SS BOND : bond 0.00648 ( 50) SS BOND : angle 1.81150 ( 100) hydrogen bonds : bond 0.04668 ( 1139) hydrogen bonds : angle 6.06562 ( 3183) link_BETA1-4 : bond 0.00787 ( 23) link_BETA1-4 : angle 3.01462 ( 69) link_NAG-ASN : bond 0.00645 ( 48) link_NAG-ASN : angle 5.06002 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 342 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1134 (ptt) cc_final: -0.0205 (mmm) REVERT: B 138 ASP cc_start: 0.5130 (t70) cc_final: 0.4730 (t0) REVERT: B 869 MET cc_start: 0.7928 (mtt) cc_final: 0.7698 (mtt) REVERT: B 902 MET cc_start: 0.8946 (tpp) cc_final: 0.8415 (tpt) REVERT: C 129 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7741 (ptmm) REVERT: C 141 LEU cc_start: 0.6133 (tp) cc_final: 0.5912 (tp) REVERT: C 236 THR cc_start: 0.8152 (t) cc_final: 0.7836 (m) REVERT: C 266 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: C 305 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7224 (t) REVERT: C 436 TRP cc_start: 0.5714 (t-100) cc_final: 0.5506 (p90) REVERT: C 547 THR cc_start: 0.7938 (m) cc_final: 0.7588 (p) REVERT: C 587 ILE cc_start: 0.9183 (mt) cc_final: 0.8916 (mt) REVERT: H 82 MET cc_start: 0.2125 (tmm) cc_final: -0.0287 (ptt) REVERT: I 118 THR cc_start: 0.3254 (OUTLIER) cc_final: 0.2719 (p) REVERT: I 132 SER cc_start: 0.4511 (OUTLIER) cc_final: 0.4241 (t) REVERT: I 140 LEU cc_start: 0.1247 (OUTLIER) cc_final: 0.0770 (mp) REVERT: I 199 ASN cc_start: 0.1609 (OUTLIER) cc_final: 0.0599 (t0) REVERT: N 110 VAL cc_start: 0.4342 (t) cc_final: 0.3699 (m) outliers start: 213 outliers final: 103 residues processed: 522 average time/residue: 0.1950 time to fit residues: 171.4825 Evaluate side-chains 357 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 247 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 166 HIS Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain I residue 27 PHE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 105 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 202 SER Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 PHE Chi-restraints excluded: chain N residue 146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 61 optimal weight: 4.9990 chunk 307 optimal weight: 10.0000 chunk 279 optimal weight: 2.9990 chunk 331 optimal weight: 7.9990 chunk 257 optimal weight: 3.9990 chunk 335 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 333 optimal weight: 8.9990 chunk 295 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN B 30 ASN B 87 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 207 HIS C 481 ASN C 493 GLN C 957 GLN C1106 GLN H 3 GLN I 81 GLN I 173 GLN M 137 ASN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.204053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.174891 restraints weight = 68305.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.170873 restraints weight = 108958.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.167634 restraints weight = 114816.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.166918 restraints weight = 112247.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.165106 restraints weight = 96389.878| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 35190 Z= 0.227 Angle : 0.870 16.632 48013 Z= 0.418 Chirality : 0.054 0.622 5628 Planarity : 0.005 0.064 6062 Dihedral : 8.712 59.921 6169 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.57 % Favored : 90.03 % Rotamer: Outliers : 5.72 % Allowed : 21.33 % Favored : 72.96 % 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: -2.14 (0.12), residues: 4244 helix: 0.41 (0.20), residues: 687 sheet: -0.43 (0.14), residues: 1213 loop : -2.67 (0.11), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 34 TYR 0.029 0.002 TYR H 33 PHE 0.022 0.002 PHE C1121 TRP 0.020 0.002 TRP I 105 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00533 (35069) covalent geometry : angle 0.82521 (47700) SS BOND : bond 0.00455 ( 50) SS BOND : angle 2.01171 ( 100) hydrogen bonds : bond 0.04837 ( 1139) hydrogen bonds : angle 5.76695 ( 3183) link_BETA1-4 : bond 0.00519 ( 23) link_BETA1-4 : angle 2.67480 ( 69) link_NAG-ASN : bond 0.01072 ( 48) link_NAG-ASN : angle 4.51459 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 261 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1106 (ptt) cc_final: 0.0242 (mmm) REVERT: A 725 GLU cc_start: 0.7648 (tt0) cc_final: 0.7423 (tt0) REVERT: B 869 MET cc_start: 0.8351 (mtt) cc_final: 0.8098 (mtt) REVERT: C 113 LYS cc_start: 0.5726 (ptpp) cc_final: 0.5346 (mttp) REVERT: C 126 VAL cc_start: 0.7299 (t) cc_final: 0.7087 (t) REVERT: C 236 THR cc_start: 0.8121 (t) cc_final: 0.7827 (m) REVERT: C 266 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: C 517 LEU cc_start: 0.4399 (OUTLIER) cc_final: 0.3751 (pt) REVERT: C 547 THR cc_start: 0.8315 (m) cc_final: 0.8024 (p) REVERT: C 787 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: C 796 ASP cc_start: 0.7151 (t0) cc_final: 0.6810 (p0) REVERT: C 1029 MET cc_start: 0.8553 (tpp) cc_final: 0.7983 (ttm) REVERT: H 122 SER cc_start: 0.5378 (t) cc_final: 0.5161 (m) REVERT: I 118 THR cc_start: 0.3156 (OUTLIER) cc_final: 0.2526 (p) REVERT: I 140 LEU cc_start: 0.1383 (OUTLIER) cc_final: 0.0770 (mp) REVERT: I 199 ASN cc_start: 0.1808 (OUTLIER) cc_final: 0.0696 (t0) REVERT: M 33 LEU cc_start: -0.0633 (OUTLIER) cc_final: -0.1087 (mt) REVERT: N 49 TYR cc_start: 0.1665 (OUTLIER) cc_final: 0.0725 (m-10) REVERT: N 110 VAL cc_start: 0.4520 (t) cc_final: 0.3782 (m) outliers start: 214 outliers final: 106 residues processed: 444 average time/residue: 0.2026 time to fit residues: 151.9726 Evaluate side-chains 335 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 221 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU 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 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 76 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 238 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 243 optimal weight: 4.9990 chunk 364 optimal weight: 5.9990 chunk 329 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 308 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 935 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS C 99 ASN C 207 HIS ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN H 173 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN M 38 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.200592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.176722 restraints weight = 67782.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.173913 restraints weight = 123713.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.171488 restraints weight = 125282.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.170557 restraints weight = 129393.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.168490 restraints weight = 111186.987| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35190 Z= 0.221 Angle : 0.837 14.721 48013 Z= 0.403 Chirality : 0.054 0.612 5628 Planarity : 0.005 0.062 6062 Dihedral : 8.323 59.964 6140 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.20 % Favored : 91.45 % Rotamer: Outliers : 6.07 % Allowed : 21.17 % Favored : 72.77 % 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: -1.87 (0.12), residues: 4244 helix: 0.59 (0.20), residues: 690 sheet: -0.31 (0.14), residues: 1242 loop : -2.47 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 108 TYR 0.022 0.002 TYR A1067 PHE 0.036 0.002 PHE N 116 TRP 0.023 0.002 TRP C 353 HIS 0.007 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00522 (35069) covalent geometry : angle 0.79860 (47700) SS BOND : bond 0.00638 ( 50) SS BOND : angle 2.17338 ( 100) hydrogen bonds : bond 0.04504 ( 1139) hydrogen bonds : angle 5.67866 ( 3183) link_BETA1-4 : bond 0.00559 ( 23) link_BETA1-4 : angle 2.43624 ( 69) link_NAG-ASN : bond 0.00817 ( 48) link_NAG-ASN : angle 4.05954 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 253 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1579 (ptt) cc_final: 0.0804 (mmm) REVERT: A 168 PHE cc_start: 0.5119 (t80) cc_final: 0.4869 (t80) REVERT: A 308 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8545 (m) REVERT: A 460 ASN cc_start: 0.6930 (m-40) cc_final: 0.6479 (m-40) REVERT: A 1029 MET cc_start: 0.8944 (tpp) cc_final: 0.8660 (ttm) REVERT: A 1130 ILE cc_start: 0.8382 (pt) cc_final: 0.8142 (mt) REVERT: B 869 MET cc_start: 0.8413 (mtt) cc_final: 0.8183 (mtt) REVERT: B 878 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8778 (tt) REVERT: B 884 SER cc_start: 0.9436 (OUTLIER) cc_final: 0.9197 (p) REVERT: C 117 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5650 (pp) REVERT: C 266 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: C 787 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7411 (mt0) REVERT: C 796 ASP cc_start: 0.7234 (t0) cc_final: 0.6819 (p0) REVERT: C 935 GLN cc_start: 0.8222 (pp30) cc_final: 0.8009 (pp30) REVERT: C 1029 MET cc_start: 0.8481 (tpp) cc_final: 0.7804 (ttm) REVERT: H 48 VAL cc_start: -0.1471 (OUTLIER) cc_final: -0.2451 (p) REVERT: I 34 MET cc_start: 0.0456 (mmt) cc_final: 0.0220 (mmt) REVERT: I 82 MET cc_start: -0.1492 (ptp) cc_final: -0.3030 (mmm) REVERT: I 118 THR cc_start: 0.3091 (OUTLIER) cc_final: 0.2471 (p) REVERT: I 199 ASN cc_start: 0.1943 (OUTLIER) cc_final: 0.1113 (t0) REVERT: M 91 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.2250 (pp) REVERT: N 49 TYR cc_start: 0.2116 (OUTLIER) cc_final: 0.0680 (m-10) REVERT: N 108 ARG cc_start: 0.1427 (OUTLIER) cc_final: 0.0667 (tmt170) REVERT: N 115 VAL cc_start: -0.0841 (OUTLIER) cc_final: -0.1045 (m) outliers start: 227 outliers final: 128 residues processed: 455 average time/residue: 0.1882 time to fit residues: 147.2950 Evaluate side-chains 343 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 202 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 146 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 50 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 332 optimal weight: 30.0000 chunk 353 optimal weight: 30.0000 chunk 210 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 318 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 542 ASN C 606 ASN C 957 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 89 GLN K 124 GLN ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 HIS N 160 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.200926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.176712 restraints weight = 67459.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.173662 restraints weight = 114234.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.171309 restraints weight = 115114.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.170504 restraints weight = 112065.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.168942 restraints weight = 106122.188| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35190 Z= 0.185 Angle : 0.774 16.683 48013 Z= 0.368 Chirality : 0.050 0.574 5628 Planarity : 0.005 0.063 6062 Dihedral : 7.858 59.910 6126 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.65 % Favored : 91.09 % Rotamer: Outliers : 5.37 % Allowed : 22.47 % Favored : 72.15 % 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: -1.68 (0.12), residues: 4244 helix: 0.84 (0.20), residues: 689 sheet: -0.22 (0.15), residues: 1220 loop : -2.34 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 97 TYR 0.021 0.002 TYR A1067 PHE 0.023 0.002 PHE B 133 TRP 0.021 0.001 TRP I 105 HIS 0.004 0.001 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00437 (35069) covalent geometry : angle 0.73574 (47700) SS BOND : bond 0.00496 ( 50) SS BOND : angle 1.82448 ( 100) hydrogen bonds : bond 0.04203 ( 1139) hydrogen bonds : angle 5.55929 ( 3183) link_BETA1-4 : bond 0.00612 ( 23) link_BETA1-4 : angle 2.33040 ( 69) link_NAG-ASN : bond 0.00595 ( 48) link_NAG-ASN : angle 3.94335 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 217 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1916 (ptt) cc_final: 0.1084 (mmm) REVERT: A 226 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7274 (mp) REVERT: A 308 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8626 (m) REVERT: A 460 ASN cc_start: 0.6646 (m-40) cc_final: 0.6345 (m-40) REVERT: A 998 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8504 (p) REVERT: A 1029 MET cc_start: 0.8937 (tpp) cc_final: 0.8716 (ttm) REVERT: B 110 LEU cc_start: 0.5519 (mp) cc_final: 0.4951 (mt) REVERT: B 189 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7006 (tp) REVERT: B 202 LYS cc_start: 0.8387 (mtpp) cc_final: 0.8051 (mtpp) REVERT: B 245 HIS cc_start: 0.4064 (OUTLIER) cc_final: 0.0788 (p-80) REVERT: B 869 MET cc_start: 0.8450 (mtt) cc_final: 0.8159 (mtt) REVERT: B 878 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8691 (tt) REVERT: C 117 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5861 (pp) REVERT: C 787 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: C 796 ASP cc_start: 0.7283 (t0) cc_final: 0.6994 (p0) REVERT: C 1029 MET cc_start: 0.8586 (tpp) cc_final: 0.8078 (ttm) REVERT: H 3 GLN cc_start: 0.6364 (mp-120) cc_final: 0.5751 (tm-30) REVERT: H 95 CYS cc_start: -0.0933 (OUTLIER) cc_final: -0.1179 (p) REVERT: I 82 MET cc_start: -0.1472 (ptp) cc_final: -0.3118 (mmm) REVERT: I 118 THR cc_start: 0.2879 (OUTLIER) cc_final: 0.2330 (p) REVERT: I 199 ASN cc_start: 0.1982 (OUTLIER) cc_final: 0.1138 (t0) REVERT: J 166 HIS cc_start: 0.1465 (OUTLIER) cc_final: 0.1200 (t-90) REVERT: N 49 TYR cc_start: 0.2156 (OUTLIER) cc_final: 0.0584 (m-10) REVERT: N 89 GLN cc_start: 0.1829 (OUTLIER) cc_final: 0.1228 (mm-40) outliers start: 201 outliers final: 137 residues processed: 395 average time/residue: 0.1904 time to fit residues: 130.3471 Evaluate side-chains 347 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 196 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 42 optimal weight: 50.0000 chunk 242 optimal weight: 0.0980 chunk 211 optimal weight: 0.8980 chunk 214 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 284 optimal weight: 0.7980 chunk 263 optimal weight: 6.9990 chunk 126 optimal weight: 0.0030 chunk 272 optimal weight: 6.9990 chunk 367 optimal weight: 20.0000 chunk 304 optimal weight: 8.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 957 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 89 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.198782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.171912 restraints weight = 66274.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.169707 restraints weight = 125845.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.166941 restraints weight = 119543.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.165546 restraints weight = 122264.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164607 restraints weight = 100580.049| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35190 Z= 0.119 Angle : 0.705 13.023 48013 Z= 0.335 Chirality : 0.048 0.532 5628 Planarity : 0.004 0.063 6062 Dihedral : 7.373 59.293 6122 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.26 % Favored : 92.48 % Rotamer: Outliers : 4.06 % Allowed : 23.38 % Favored : 72.55 % 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: -1.39 (0.13), residues: 4244 helix: 1.17 (0.21), residues: 688 sheet: -0.07 (0.15), residues: 1207 loop : -2.14 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.024 0.001 TYR M 32 PHE 0.023 0.001 PHE I 102 TRP 0.017 0.001 TRP I 105 HIS 0.032 0.001 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00265 (35069) covalent geometry : angle 0.67095 (47700) SS BOND : bond 0.00344 ( 50) SS BOND : angle 1.62226 ( 100) hydrogen bonds : bond 0.03562 ( 1139) hydrogen bonds : angle 5.28318 ( 3183) link_BETA1-4 : bond 0.00540 ( 23) link_BETA1-4 : angle 2.21163 ( 69) link_NAG-ASN : bond 0.00576 ( 48) link_NAG-ASN : angle 3.51133 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 229 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1809 (ptt) cc_final: 0.0989 (mmm) REVERT: A 308 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8549 (m) REVERT: A 389 ASP cc_start: 0.5569 (OUTLIER) cc_final: 0.5129 (m-30) REVERT: A 460 ASN cc_start: 0.6750 (m-40) cc_final: 0.6425 (m-40) REVERT: A 1029 MET cc_start: 0.8653 (tpp) cc_final: 0.8419 (ttm) REVERT: B 110 LEU cc_start: 0.4977 (mp) cc_final: 0.4599 (mt) REVERT: B 189 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6946 (tp) REVERT: B 245 HIS cc_start: 0.4017 (OUTLIER) cc_final: 0.0695 (p-80) REVERT: B 878 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8821 (tt) REVERT: C 117 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5603 (pp) REVERT: C 266 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7134 (m-80) REVERT: C 787 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: C 1029 MET cc_start: 0.8336 (tpp) cc_final: 0.7856 (ttm) REVERT: H 3 GLN cc_start: 0.6181 (mp-120) cc_final: 0.5666 (tm-30) REVERT: H 95 CYS cc_start: -0.1056 (OUTLIER) cc_final: -0.1288 (p) REVERT: I 82 MET cc_start: -0.1704 (ptp) cc_final: -0.3235 (mmm) REVERT: I 118 THR cc_start: 0.2823 (OUTLIER) cc_final: 0.2282 (p) REVERT: I 199 ASN cc_start: 0.1641 (OUTLIER) cc_final: 0.0885 (t0) REVERT: J 18 LEU cc_start: 0.1002 (tp) cc_final: 0.0557 (mp) REVERT: N 32 TYR cc_start: 0.2416 (OUTLIER) cc_final: 0.2144 (p90) REVERT: N 49 TYR cc_start: 0.2110 (OUTLIER) cc_final: 0.0676 (m-10) REVERT: N 89 GLN cc_start: 0.1695 (OUTLIER) cc_final: 0.1052 (tp40) outliers start: 152 outliers final: 101 residues processed: 364 average time/residue: 0.1972 time to fit residues: 123.4232 Evaluate side-chains 313 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 198 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 203 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 105 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 314 optimal weight: 7.9990 chunk 393 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 361 optimal weight: 40.0000 chunk 183 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A1135 ASN B 134 GLN B 334 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN C 751 ASN C 804 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 GLN ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.192710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.162983 restraints weight = 66324.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.162028 restraints weight = 119805.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159504 restraints weight = 110253.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.157354 restraints weight = 123578.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.156376 restraints weight = 109905.869| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 35190 Z= 0.272 Angle : 0.868 15.204 48013 Z= 0.418 Chirality : 0.055 0.681 5628 Planarity : 0.005 0.066 6062 Dihedral : 8.301 58.283 6119 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.57 % Favored : 90.15 % Rotamer: Outliers : 5.10 % Allowed : 23.22 % Favored : 71.67 % 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: -1.71 (0.12), residues: 4244 helix: 0.66 (0.20), residues: 687 sheet: -0.28 (0.15), residues: 1247 loop : -2.30 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 44 TYR 0.023 0.002 TYR I 33 PHE 0.027 0.002 PHE A 86 TRP 0.018 0.002 TRP J 105 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00654 (35069) covalent geometry : angle 0.82979 (47700) SS BOND : bond 0.00513 ( 50) SS BOND : angle 2.14637 ( 100) hydrogen bonds : bond 0.05105 ( 1139) hydrogen bonds : angle 5.79570 ( 3183) link_BETA1-4 : bond 0.00474 ( 23) link_BETA1-4 : angle 2.36015 ( 69) link_NAG-ASN : bond 0.00680 ( 48) link_NAG-ASN : angle 4.13573 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 214 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1622 (ptt) cc_final: 0.1217 (mmm) REVERT: A 308 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8699 (m) REVERT: A 460 ASN cc_start: 0.7065 (m-40) cc_final: 0.6617 (m-40) REVERT: A 998 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8570 (p) REVERT: B 110 LEU cc_start: 0.5920 (mp) cc_final: 0.5235 (mt) REVERT: B 189 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7254 (tp) REVERT: B 245 HIS cc_start: 0.3881 (OUTLIER) cc_final: 0.0693 (p-80) REVERT: C 66 HIS cc_start: 0.6011 (OUTLIER) cc_final: 0.5493 (t-90) REVERT: C 117 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6210 (pp) REVERT: C 266 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.6759 (m-80) REVERT: C 787 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7530 (mt0) REVERT: C 1021 SER cc_start: 0.9202 (OUTLIER) cc_final: 0.8699 (t) REVERT: C 1029 MET cc_start: 0.8555 (tpp) cc_final: 0.8253 (ttm) REVERT: H 3 GLN cc_start: 0.6513 (mp-120) cc_final: 0.5715 (tm-30) REVERT: K 20 THR cc_start: 0.2908 (OUTLIER) cc_final: 0.2266 (t) REVERT: I 82 MET cc_start: -0.1442 (ptp) cc_final: -0.2898 (mmm) REVERT: M 89 GLN cc_start: 0.4063 (OUTLIER) cc_final: 0.3789 (tt0) REVERT: M 91 LEU cc_start: 0.3054 (OUTLIER) cc_final: 0.2402 (pp) REVERT: M 188 LYS cc_start: 0.4323 (mtmm) cc_final: 0.3902 (mtmt) REVERT: N 32 TYR cc_start: 0.2701 (OUTLIER) cc_final: 0.2279 (p90) REVERT: N 49 TYR cc_start: 0.1824 (OUTLIER) cc_final: 0.0291 (m-10) REVERT: N 89 GLN cc_start: 0.2181 (OUTLIER) cc_final: 0.1698 (mm-40) outliers start: 191 outliers final: 131 residues processed: 386 average time/residue: 0.1910 time to fit residues: 128.1108 Evaluate side-chains 334 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 188 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL 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 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 203 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 200 optimal weight: 10.0000 chunk 297 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 305 optimal weight: 0.0050 chunk 346 optimal weight: 6.9990 chunk 423 optimal weight: 40.0000 chunk 154 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN B 81 ASN B 481 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 160 GLN ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 GLN J 157 ASN J 166 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.194433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.166395 restraints weight = 66274.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.163199 restraints weight = 114286.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.160801 restraints weight = 115210.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.159870 restraints weight = 126053.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157551 restraints weight = 112335.631| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.6734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35190 Z= 0.162 Angle : 0.748 13.637 48013 Z= 0.356 Chirality : 0.050 0.563 5628 Planarity : 0.005 0.064 6062 Dihedral : 7.773 59.421 6117 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.35 % Favored : 92.41 % Rotamer: Outliers : 4.44 % Allowed : 24.37 % Favored : 71.19 % 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: -1.55 (0.13), residues: 4244 helix: 0.93 (0.20), residues: 701 sheet: -0.24 (0.15), residues: 1236 loop : -2.20 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.023 0.001 TYR M 32 PHE 0.022 0.002 PHE A 238 TRP 0.040 0.002 TRP A 436 HIS 0.003 0.001 HIS J 202 Details of bonding type rmsd covalent geometry : bond 0.00380 (35069) covalent geometry : angle 0.71302 (47700) SS BOND : bond 0.00404 ( 50) SS BOND : angle 1.75138 ( 100) hydrogen bonds : bond 0.04029 ( 1139) hydrogen bonds : angle 5.49902 ( 3183) link_BETA1-4 : bond 0.00501 ( 23) link_BETA1-4 : angle 2.15728 ( 69) link_NAG-ASN : bond 0.00601 ( 48) link_NAG-ASN : angle 3.68350 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 201 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1854 (ptt) cc_final: 0.1543 (mmm) REVERT: A 308 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8644 (m) REVERT: A 460 ASN cc_start: 0.7074 (m-40) cc_final: 0.6588 (m-40) REVERT: A 1029 MET cc_start: 0.8429 (tpp) cc_final: 0.8111 (ttm) REVERT: B 110 LEU cc_start: 0.5687 (mp) cc_final: 0.5288 (mt) REVERT: B 189 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7330 (tp) REVERT: B 245 HIS cc_start: 0.4180 (OUTLIER) cc_final: 0.0692 (p-80) REVERT: B 878 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8765 (tt) REVERT: C 66 HIS cc_start: 0.5866 (OUTLIER) cc_final: 0.5285 (t-90) REVERT: C 117 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6104 (pp) REVERT: C 190 ARG cc_start: 0.6605 (mmt180) cc_final: 0.6143 (mmm-85) REVERT: C 266 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.6267 (m-80) REVERT: C 787 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: C 1021 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8512 (t) REVERT: C 1029 MET cc_start: 0.8676 (tpp) cc_final: 0.8215 (ttm) REVERT: H 3 GLN cc_start: 0.6453 (mp-120) cc_final: 0.5671 (tm-30) REVERT: I 82 MET cc_start: -0.1526 (ptp) cc_final: -0.3075 (mmm) REVERT: M 91 LEU cc_start: 0.2830 (OUTLIER) cc_final: 0.2419 (pp) REVERT: J 18 LEU cc_start: 0.1235 (tp) cc_final: 0.0799 (pp) REVERT: N 32 TYR cc_start: 0.2606 (OUTLIER) cc_final: 0.2181 (p90) REVERT: N 49 TYR cc_start: 0.1395 (OUTLIER) cc_final: 0.0175 (m-10) REVERT: N 89 GLN cc_start: 0.1940 (OUTLIER) cc_final: 0.1421 (mm-40) outliers start: 166 outliers final: 128 residues processed: 353 average time/residue: 0.1973 time to fit residues: 120.9470 Evaluate side-chains 327 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 186 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 213 VAL 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 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain M residue 155 GLN Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 203 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 143 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 418 optimal weight: 20.0000 chunk 417 optimal weight: 0.6980 chunk 382 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 272 optimal weight: 0.6980 chunk 310 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 89 GLN ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.195534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.166540 restraints weight = 65978.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.164320 restraints weight = 122089.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162793 restraints weight = 104471.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161239 restraints weight = 117774.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159851 restraints weight = 110450.856| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35190 Z= 0.131 Angle : 0.718 12.523 48013 Z= 0.343 Chirality : 0.049 0.539 5628 Planarity : 0.004 0.057 6062 Dihedral : 7.417 58.887 6117 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.18 % Favored : 91.59 % Rotamer: Outliers : 3.71 % Allowed : 25.12 % Favored : 71.17 % 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: -1.35 (0.13), residues: 4244 helix: 1.14 (0.20), residues: 702 sheet: -0.11 (0.15), residues: 1226 loop : -2.09 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.023 0.001 TYR M 49 PHE 0.022 0.001 PHE C 855 TRP 0.033 0.001 TRP A 436 HIS 0.003 0.001 HIS J 202 Details of bonding type rmsd covalent geometry : bond 0.00301 (35069) covalent geometry : angle 0.68717 (47700) SS BOND : bond 0.00398 ( 50) SS BOND : angle 1.66928 ( 100) hydrogen bonds : bond 0.03690 ( 1139) hydrogen bonds : angle 5.32475 ( 3183) link_BETA1-4 : bond 0.00545 ( 23) link_BETA1-4 : angle 2.08085 ( 69) link_NAG-ASN : bond 0.00549 ( 48) link_NAG-ASN : angle 3.37310 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 205 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5547 (OUTLIER) cc_final: 0.3945 (tttt) REVERT: A 153 MET cc_start: 0.1957 (ptt) cc_final: 0.1645 (mmm) REVERT: A 308 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8668 (m) REVERT: A 460 ASN cc_start: 0.7190 (m-40) cc_final: 0.6712 (m-40) REVERT: A 1029 MET cc_start: 0.8611 (tpp) cc_final: 0.8388 (ttm) REVERT: B 189 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7401 (tp) REVERT: B 245 HIS cc_start: 0.4149 (OUTLIER) cc_final: 0.0601 (p-80) REVERT: C 66 HIS cc_start: 0.5794 (OUTLIER) cc_final: 0.5072 (t-90) REVERT: C 117 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5996 (pp) REVERT: C 266 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: C 787 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: C 1029 MET cc_start: 0.8521 (tpp) cc_final: 0.8159 (ttm) REVERT: H 3 GLN cc_start: 0.6440 (mp-120) cc_final: 0.5675 (tm-30) REVERT: H 95 CYS cc_start: -0.0502 (OUTLIER) cc_final: -0.0801 (p) REVERT: I 82 MET cc_start: -0.1522 (ptp) cc_final: -0.3128 (mmm) REVERT: M 91 LEU cc_start: 0.2778 (OUTLIER) cc_final: 0.2379 (pp) REVERT: J 18 LEU cc_start: 0.1346 (tp) cc_final: 0.0924 (pp) REVERT: N 32 TYR cc_start: 0.2061 (OUTLIER) cc_final: 0.1535 (p90) REVERT: N 49 TYR cc_start: 0.1269 (OUTLIER) cc_final: 0.0103 (m-10) REVERT: N 89 GLN cc_start: 0.2046 (OUTLIER) cc_final: 0.1629 (mm-40) outliers start: 139 outliers final: 111 residues processed: 325 average time/residue: 0.1895 time to fit residues: 106.3968 Evaluate side-chains 316 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 192 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL 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 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 105 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 227 optimal weight: 0.9990 chunk 408 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 423 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 375 optimal weight: 20.0000 chunk 175 optimal weight: 0.9990 chunk 327 optimal weight: 40.0000 chunk 246 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 81 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.194298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.164809 restraints weight = 66039.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162026 restraints weight = 128135.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.160479 restraints weight = 130429.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.159691 restraints weight = 118400.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.158791 restraints weight = 116509.226| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35190 Z= 0.162 Angle : 0.736 13.076 48013 Z= 0.350 Chirality : 0.049 0.561 5628 Planarity : 0.005 0.057 6062 Dihedral : 7.447 59.744 6114 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.06 % Favored : 91.71 % Rotamer: Outliers : 3.66 % Allowed : 25.15 % Favored : 71.19 % 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: -1.37 (0.13), residues: 4244 helix: 1.10 (0.20), residues: 702 sheet: -0.13 (0.15), residues: 1215 loop : -2.08 (0.12), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.027 0.002 TYR M 49 PHE 0.023 0.002 PHE B 133 TRP 0.030 0.002 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00382 (35069) covalent geometry : angle 0.70290 (47700) SS BOND : bond 0.00435 ( 50) SS BOND : angle 1.69568 ( 100) hydrogen bonds : bond 0.03910 ( 1139) hydrogen bonds : angle 5.35741 ( 3183) link_BETA1-4 : bond 0.00526 ( 23) link_BETA1-4 : angle 2.07990 ( 69) link_NAG-ASN : bond 0.00778 ( 48) link_NAG-ASN : angle 3.59006 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 197 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5623 (OUTLIER) cc_final: 0.4009 (ttmt) REVERT: A 226 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7174 (mp) REVERT: A 308 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8664 (m) REVERT: A 460 ASN cc_start: 0.7074 (m-40) cc_final: 0.6591 (m-40) REVERT: B 189 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7381 (tp) REVERT: B 245 HIS cc_start: 0.4152 (OUTLIER) cc_final: 0.0596 (p-80) REVERT: C 66 HIS cc_start: 0.5900 (OUTLIER) cc_final: 0.4992 (t-90) REVERT: C 266 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.5976 (m-80) REVERT: C 787 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: C 1029 MET cc_start: 0.8198 (tpp) cc_final: 0.7994 (ttm) REVERT: H 3 GLN cc_start: 0.6476 (mp-120) cc_final: 0.5687 (tm-30) REVERT: I 82 MET cc_start: -0.1505 (ptp) cc_final: -0.3226 (mmm) REVERT: M 91 LEU cc_start: 0.2909 (OUTLIER) cc_final: 0.2467 (pp) REVERT: J 18 LEU cc_start: 0.1616 (tp) cc_final: 0.1117 (pp) REVERT: N 49 TYR cc_start: 0.1296 (OUTLIER) cc_final: 0.0220 (t80) REVERT: N 89 GLN cc_start: 0.2269 (OUTLIER) cc_final: 0.1894 (mm-40) REVERT: N 108 ARG cc_start: 0.2196 (OUTLIER) cc_final: 0.1362 (tmt170) outliers start: 137 outliers final: 117 residues processed: 319 average time/residue: 0.1835 time to fit residues: 102.1135 Evaluate side-chains 318 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 189 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 105 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 292 optimal weight: 0.9990 chunk 307 optimal weight: 9.9990 chunk 408 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 281 optimal weight: 0.8980 chunk 327 optimal weight: 40.0000 chunk 130 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 349 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.194505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.167483 restraints weight = 65873.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.164114 restraints weight = 100741.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.160545 restraints weight = 98730.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.159828 restraints weight = 114332.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.158023 restraints weight = 94630.691| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.7129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35190 Z= 0.148 Angle : 0.728 13.836 48013 Z= 0.347 Chirality : 0.049 0.545 5628 Planarity : 0.005 0.054 6062 Dihedral : 7.312 59.390 6114 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.20 % Favored : 91.61 % Rotamer: Outliers : 4.04 % Allowed : 24.77 % Favored : 71.19 % 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: -1.32 (0.13), residues: 4244 helix: 1.18 (0.20), residues: 702 sheet: -0.09 (0.15), residues: 1178 loop : -2.04 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.025 0.001 TYR M 32 PHE 0.036 0.002 PHE C 65 TRP 0.030 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00344 (35069) covalent geometry : angle 0.69562 (47700) SS BOND : bond 0.00371 ( 50) SS BOND : angle 1.84578 ( 100) hydrogen bonds : bond 0.03766 ( 1139) hydrogen bonds : angle 5.29622 ( 3183) link_BETA1-4 : bond 0.00485 ( 23) link_BETA1-4 : angle 2.05220 ( 69) link_NAG-ASN : bond 0.00623 ( 48) link_NAG-ASN : angle 3.47266 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5479.29 seconds wall clock time: 96 minutes 8.09 seconds (5768.09 seconds total)