Starting phenix.real_space_refine on Sun Jun 29 07:56:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7czs_30515/06_2025/7czs_30515.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czs_30515/06_2025/7czs_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_30515/06_2025/7czs_30515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czs_30515/06_2025/7czs_30515.map" model { file = "/net/cci-nas-00/data/ceres_data/7czs_30515/06_2025/7czs_30515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czs_30515/06_2025/7czs_30515.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.79, per 1000 atoms: 0.55 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: 8.28 Conformation dependent library (CDL) restraints added in 4.0 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: 4.78 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: 16.22 Time building geometry restraints manager: 9.82 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 1146 or resid 1401 through 1410)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1410)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1146 or resid 1401 thr \ ough 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: 0.010 Normalize map: mean=0, sd=1: 1.140 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: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 76.100 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.230 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.980 ------------------------------------------------------------------------------- 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 : 35.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.166 0.005 TRP C 64 HIS 0.009 0.002 HIS B 207 PHE 0.119 0.005 PHE C 220 TYR 0.091 0.003 TYR C 38 ARG 0.011 0.001 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.06537 ( 48) link_NAG-ASN : angle 11.46813 ( 144) link_BETA1-4 : bond 0.09999 ( 23) link_BETA1-4 : angle 11.29437 ( 69) hydrogen bonds : bond 0.21339 ( 1139) hydrogen bonds : angle 8.58059 ( 3183) SS BOND : bond 0.09849 ( 50) SS BOND : angle 11.36433 ( 100) covalent geometry : bond 0.01263 (35069) covalent geometry : angle 1.30113 (47700) *********************** 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 : 3.410 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: 0.8075 (mt) REVERT: A 203 ILE cc_start: 0.7006 (mt) cc_final: 0.6709 (mt) REVERT: A 231 ILE cc_start: 0.4068 (OUTLIER) cc_final: 0.3696 (mt) REVERT: A 438 SER cc_start: 0.1285 (OUTLIER) cc_final: 0.0151 (m) REVERT: A 537 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6708 (mtpp) REVERT: A 939 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.7380 (m) REVERT: A 998 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8382 (p) REVERT: B 114 THR cc_start: 0.2564 (OUTLIER) cc_final: 0.2361 (m) REVERT: B 212 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.4609 (pp) REVERT: B 214 ARG cc_start: 0.0733 (OUTLIER) cc_final: -0.0100 (ttm110) REVERT: B 459 SER cc_start: 0.4892 (OUTLIER) cc_final: 0.4583 (m) REVERT: B 517 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.4167 (pt) REVERT: B 540 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6673 (t0) REVERT: B 588 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8313 (m) REVERT: B 591 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8122 (m) REVERT: B 697 MET cc_start: 0.7834 (ptm) cc_final: 0.7565 (ptp) REVERT: B 869 MET cc_start: 0.7766 (mtt) cc_final: 0.7518 (mtt) REVERT: B 917 TYR cc_start: 0.8366 (m-80) cc_final: 0.8107 (m-80) REVERT: C 305 SER cc_start: 0.7047 (OUTLIER) cc_final: 0.6755 (t) REVERT: C 517 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5517 (mp) REVERT: C 547 THR cc_start: 0.7538 (m) cc_final: 0.7113 (p) REVERT: C 699 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8438 (mt) REVERT: C 787 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7274 (mt0) REVERT: C 794 ILE cc_start: 0.7680 (mp) cc_final: 0.7437 (tt) REVERT: C 814 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.6225 (ptpt) REVERT: C 904 TYR cc_start: 0.8019 (m-10) cc_final: 0.7807 (m-10) REVERT: C 917 TYR cc_start: 0.8668 (m-80) cc_final: 0.8298 (m-80) REVERT: H 33 TYR cc_start: 0.3049 (m-80) cc_final: 0.2174 (m-80) REVERT: H 82 MET cc_start: -0.1465 (ptp) cc_final: -0.2229 (ptp) REVERT: H 158 SER cc_start: 0.1954 (OUTLIER) cc_final: 0.1663 (p) REVERT: I 140 LEU cc_start: 0.0697 (OUTLIER) cc_final: 0.0127 (mp) REVERT: I 158 SER cc_start: 0.2620 (OUTLIER) cc_final: 0.2298 (m) REVERT: I 199 ASN cc_start: 0.3497 (OUTLIER) cc_final: 0.2383 (t0) REVERT: M 63 SER cc_start: 0.4912 (OUTLIER) cc_final: 0.4667 (m) REVERT: J 63 VAL cc_start: 0.0504 (OUTLIER) cc_final: 0.0121 (m) REVERT: J 100 LEU cc_start: 0.2930 (OUTLIER) cc_final: 0.2700 (mt) REVERT: N 49 TYR cc_start: 0.3254 (OUTLIER) cc_final: 0.2875 (t80) REVERT: N 54 LEU cc_start: 0.1427 (OUTLIER) cc_final: 0.0629 (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: 0.4570 time to fit residues: 720.1054 Evaluate side-chains 397 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 287 time to evaluate : 3.773 ------------------------------------------------------------------------------- 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 212 LEU 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 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 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 359 optimal weight: 10.0000 chunk 322 optimal weight: 30.0000 chunk 179 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 333 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 386 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 440 ASN A 450 ASN A 498 GLN A 644 GLN A 658 ASN 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 493 GLN 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 C1106 GLN K 90 GLN M 37 GLN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.209228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178772 restraints weight = 67269.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.174769 restraints weight = 115721.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.171902 restraints weight = 118080.232| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.3113 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= 0.188 Angle : 0.920 17.577 48013 Z= 0.443 Chirality : 0.055 0.824 5628 Planarity : 0.006 0.062 6062 Dihedral : 9.575 60.474 6287 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.48 % Favored : 90.90 % Rotamer: Outliers : 5.80 % Allowed : 19.67 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.12), residues: 4244 helix: -0.25 (0.19), residues: 695 sheet: -0.87 (0.14), residues: 1203 loop : -2.92 (0.11), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 105 HIS 0.009 0.001 HIS A 519 PHE 0.025 0.002 PHE B 86 TYR 0.030 0.002 TYR M 32 ARG 0.008 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 48) link_NAG-ASN : angle 5.05498 ( 144) link_BETA1-4 : bond 0.00687 ( 23) link_BETA1-4 : angle 3.15480 ( 69) hydrogen bonds : bond 0.04830 ( 1139) hydrogen bonds : angle 6.08339 ( 3183) SS BOND : bond 0.00484 ( 50) SS BOND : angle 1.84978 ( 100) covalent geometry : bond 0.00426 (35069) covalent geometry : angle 0.86776 (47700) *********************** 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 554 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 337 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0975 (ptt) cc_final: 0.0112 (mmm) REVERT: A 725 GLU cc_start: 0.7480 (tt0) cc_final: 0.7156 (tt0) REVERT: B 138 ASP cc_start: 0.5032 (t70) cc_final: 0.4622 (t0) REVERT: B 212 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.5060 (pp) REVERT: B 266 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: B 869 MET cc_start: 0.8029 (mtt) cc_final: 0.7773 (mtt) REVERT: B 902 MET cc_start: 0.8880 (tpp) cc_final: 0.8337 (tpt) REVERT: C 129 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7750 (ptmm) REVERT: C 236 THR cc_start: 0.8143 (t) cc_final: 0.7847 (m) REVERT: C 266 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6363 (m-80) REVERT: C 305 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7356 (t) REVERT: C 517 LEU cc_start: 0.4382 (OUTLIER) cc_final: 0.3628 (pt) REVERT: C 547 THR cc_start: 0.7973 (m) cc_final: 0.7633 (p) REVERT: C 587 ILE cc_start: 0.9206 (mt) cc_final: 0.8961 (mt) REVERT: C 787 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7215 (mt0) REVERT: I 118 THR cc_start: 0.3205 (OUTLIER) cc_final: 0.2640 (p) REVERT: I 140 LEU cc_start: 0.1274 (OUTLIER) cc_final: 0.0761 (mp) REVERT: I 199 ASN cc_start: 0.1544 (OUTLIER) cc_final: 0.0567 (t0) REVERT: N 91 LEU cc_start: -0.0991 (OUTLIER) cc_final: -0.1318 (pp) REVERT: N 110 VAL cc_start: 0.4379 (t) cc_final: 0.3738 (m) outliers start: 217 outliers final: 103 residues processed: 520 average time/residue: 0.4757 time to fit residues: 420.7360 Evaluate side-chains 359 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 245 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 122 ASN 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 699 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE 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 212 LEU 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 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 197 ILE 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 289 VAL 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 517 LEU 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 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 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 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 50 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 367 optimal weight: 7.9990 chunk 338 optimal weight: 20.0000 chunk 284 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 346 optimal weight: 0.6980 chunk 313 optimal weight: 40.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A1071 GLN 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 H 81 GLN I 81 GLN I 173 GLN M 137 ASN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN N 137 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.204648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.180053 restraints weight = 68338.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.177115 restraints weight = 129962.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.175213 restraints weight = 110017.874| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 35190 Z= 0.203 Angle : 0.846 20.284 48013 Z= 0.408 Chirality : 0.053 0.550 5628 Planarity : 0.005 0.064 6062 Dihedral : 8.650 59.524 6174 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.40 % Favored : 90.20 % Rotamer: Outliers : 5.91 % Allowed : 20.92 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.12), residues: 4244 helix: 0.51 (0.20), residues: 688 sheet: -0.45 (0.14), residues: 1224 loop : -2.58 (0.11), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 436 HIS 0.008 0.001 HIS A 519 PHE 0.029 0.002 PHE J 27 TYR 0.032 0.002 TYR H 33 ARG 0.008 0.001 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 48) link_NAG-ASN : angle 4.24827 ( 144) link_BETA1-4 : bond 0.00512 ( 23) link_BETA1-4 : angle 2.63263 ( 69) hydrogen bonds : bond 0.04665 ( 1139) hydrogen bonds : angle 5.71014 ( 3183) SS BOND : bond 0.00429 ( 50) SS BOND : angle 1.91617 ( 100) covalent geometry : bond 0.00473 (35069) covalent geometry : angle 0.80535 (47700) *********************** 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 480 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 259 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1281 (ptt) cc_final: 0.0204 (mmm) REVERT: A 725 GLU cc_start: 0.7633 (tt0) cc_final: 0.7422 (tt0) REVERT: A 998 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8420 (p) REVERT: B 389 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6005 (p0) REVERT: B 869 MET cc_start: 0.8290 (mtt) cc_final: 0.8031 (mtt) REVERT: B 1106 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.9006 (pt0) REVERT: C 126 VAL cc_start: 0.7255 (t) cc_final: 0.7027 (t) REVERT: C 236 THR cc_start: 0.8115 (t) cc_final: 0.7874 (m) REVERT: C 266 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: C 517 LEU cc_start: 0.4206 (OUTLIER) cc_final: 0.3655 (pt) REVERT: C 547 THR cc_start: 0.8263 (m) cc_final: 0.7961 (p) REVERT: C 787 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7303 (mt0) REVERT: C 796 ASP cc_start: 0.7084 (t0) cc_final: 0.6671 (p0) REVERT: C 1029 MET cc_start: 0.8386 (tpp) cc_final: 0.7901 (ttm) REVERT: H 82 MET cc_start: 0.2464 (ptp) cc_final: 0.1498 (ptp) REVERT: H 122 SER cc_start: 0.5167 (t) cc_final: 0.4953 (m) REVERT: I 118 THR cc_start: 0.3129 (OUTLIER) cc_final: 0.2482 (p) REVERT: I 140 LEU cc_start: 0.1572 (OUTLIER) cc_final: 0.1004 (mp) REVERT: I 199 ASN cc_start: 0.1720 (OUTLIER) cc_final: 0.0763 (t0) REVERT: M 33 LEU cc_start: -0.0922 (OUTLIER) cc_final: -0.1283 (mt) REVERT: M 137 ASN cc_start: 0.2357 (OUTLIER) cc_final: 0.1819 (t0) REVERT: J 82 MET cc_start: -0.0974 (mtm) cc_final: -0.1228 (mtm) REVERT: N 49 TYR cc_start: 0.1538 (OUTLIER) cc_final: 0.0609 (m-10) REVERT: N 110 VAL cc_start: 0.4478 (t) cc_final: 0.4058 (m) outliers start: 221 outliers final: 110 residues processed: 450 average time/residue: 0.4155 time to fit residues: 316.7066 Evaluate side-chains 343 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 221 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL 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 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 371 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 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 699 LEU 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 985 ASP 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 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP 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 523 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 580 GLN 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 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 854 LYS 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 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 1106 GLN 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 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR 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 913 GLN 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 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 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 114 SER Chi-restraints excluded: chain M residue 137 ASN 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 174 optimal weight: 1.9990 chunk 365 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 209 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 373 optimal weight: 5.9990 chunk 299 optimal weight: 8.9990 chunk 300 optimal weight: 20.0000 chunk 175 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 751 ASN B 30 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B1058 HIS C 606 ASN C 804 GLN C 957 GLN H 173 GLN K 6 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.201260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.177181 restraints weight = 67946.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.174456 restraints weight = 124812.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.171823 restraints weight = 110082.373| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35190 Z= 0.216 Angle : 0.814 15.233 48013 Z= 0.391 Chirality : 0.053 0.654 5628 Planarity : 0.005 0.060 6062 Dihedral : 8.206 59.903 6142 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.29 % Favored : 91.35 % Rotamer: Outliers : 5.72 % Allowed : 21.25 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.12), residues: 4244 helix: 0.63 (0.20), residues: 688 sheet: -0.25 (0.15), residues: 1223 loop : -2.42 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 105 HIS 0.005 0.001 HIS A 245 PHE 0.027 0.002 PHE B 855 TYR 0.025 0.002 TYR B 904 ARG 0.005 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 48) link_NAG-ASN : angle 4.21115 ( 144) link_BETA1-4 : bond 0.00812 ( 23) link_BETA1-4 : angle 2.45444 ( 69) hydrogen bonds : bond 0.04447 ( 1139) hydrogen bonds : angle 5.60651 ( 3183) SS BOND : bond 0.00881 ( 50) SS BOND : angle 2.11360 ( 100) covalent geometry : bond 0.00505 (35069) covalent geometry : angle 0.77191 (47700) *********************** 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 472 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 258 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1565 (ptt) cc_final: 0.0794 (mmm) REVERT: A 1029 MET cc_start: 0.8931 (tpp) cc_final: 0.8618 (ttm) REVERT: A 1130 ILE cc_start: 0.8424 (pt) cc_final: 0.8127 (mt) REVERT: B 266 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: B 389 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6117 (p0) REVERT: B 869 MET cc_start: 0.8397 (mtt) cc_final: 0.8150 (mtt) REVERT: C 236 THR cc_start: 0.8139 (t) cc_final: 0.7854 (m) REVERT: C 266 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: C 796 ASP cc_start: 0.7337 (t0) cc_final: 0.6797 (p0) REVERT: C 935 GLN cc_start: 0.8223 (pp30) cc_final: 0.8003 (pp30) REVERT: C 1029 MET cc_start: 0.8354 (tpp) cc_final: 0.7767 (ttm) REVERT: I 34 MET cc_start: 0.0301 (mmt) cc_final: 0.0039 (mmt) REVERT: I 82 MET cc_start: -0.1434 (ptp) cc_final: -0.3096 (mmm) REVERT: I 118 THR cc_start: 0.3197 (OUTLIER) cc_final: 0.2566 (p) REVERT: I 199 ASN cc_start: 0.1844 (OUTLIER) cc_final: 0.1006 (t0) REVERT: M 91 LEU cc_start: 0.2637 (OUTLIER) cc_final: 0.2120 (pp) REVERT: N 49 TYR cc_start: 0.1838 (OUTLIER) cc_final: 0.0596 (m-10) REVERT: N 115 VAL cc_start: -0.0750 (OUTLIER) cc_final: -0.0987 (m) outliers start: 214 outliers final: 125 residues processed: 448 average time/residue: 0.4234 time to fit residues: 324.7582 Evaluate side-chains 339 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 206 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 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 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 403 ARG Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 618 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 931 ILE Chi-restraints excluded: chain A residue 937 SER 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 114 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 389 ASP 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 523 THR Chi-restraints excluded: chain B residue 554 GLU 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 708 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 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 1136 THR Chi-restraints excluded: chain C residue 83 VAL 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 267 VAL 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 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 620 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 753 LEU 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 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 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 92 VAL 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 129 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 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 M residue 116 PHE 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 137 THR Chi-restraints excluded: chain J residue 144 VAL 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 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 83 optimal weight: 0.7980 chunk 141 optimal weight: 20.0000 chunk 389 optimal weight: 0.0770 chunk 377 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 387 optimal weight: 40.0000 chunk 40 optimal weight: 40.0000 chunk 339 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 overall best weight: 4.3744 ------------------------------------------------------------------------------- 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 487 ASN B 218 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 607 GLN C 957 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 GLN ** 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 = 0.4496 r_free = 0.4496 target = 0.199232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.173815 restraints weight = 67452.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.170945 restraints weight = 128494.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.168943 restraints weight = 114257.720| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35190 Z= 0.219 Angle : 0.812 14.482 48013 Z= 0.388 Chirality : 0.052 0.589 5628 Planarity : 0.005 0.064 6062 Dihedral : 7.990 58.779 6131 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.93 % Favored : 90.79 % Rotamer: Outliers : 5.59 % Allowed : 22.42 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.12), residues: 4244 helix: 0.63 (0.20), residues: 694 sheet: -0.19 (0.15), residues: 1209 loop : -2.33 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 105 HIS 0.005 0.001 HIS J 166 PHE 0.031 0.002 PHE H 102 TYR 0.035 0.002 TYR B 904 ARG 0.007 0.001 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 48) link_NAG-ASN : angle 3.86574 ( 144) link_BETA1-4 : bond 0.00560 ( 23) link_BETA1-4 : angle 2.36617 ( 69) hydrogen bonds : bond 0.04453 ( 1139) hydrogen bonds : angle 5.61156 ( 3183) SS BOND : bond 0.00609 ( 50) SS BOND : angle 1.87500 ( 100) covalent geometry : bond 0.00518 (35069) covalent geometry : angle 0.77651 (47700) *********************** 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 442 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 233 time to evaluate : 3.403 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 153 MET cc_start: 0.1752 (ptt) cc_final: 0.0988 (mmm) REVERT: A 308 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8672 (m) REVERT: A 460 ASN cc_start: 0.6756 (m-40) cc_final: 0.6457 (m-40) REVERT: A 998 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8509 (p) REVERT: A 1029 MET cc_start: 0.8900 (tpp) cc_final: 0.8682 (ttm) REVERT: B 245 HIS cc_start: 0.4099 (OUTLIER) cc_final: 0.0824 (p-80) REVERT: B 266 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8337 (m-80) REVERT: B 389 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6250 (p0) REVERT: B 869 MET cc_start: 0.8436 (mtt) cc_final: 0.8139 (mtt) REVERT: B 878 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8701 (tt) REVERT: B 902 MET cc_start: 0.8840 (tpp) cc_final: 0.8632 (mmt) REVERT: C 233 ILE cc_start: 0.7188 (OUTLIER) cc_final: 0.6908 (mt) REVERT: C 796 ASP cc_start: 0.7295 (t0) cc_final: 0.6958 (p0) REVERT: C 1029 MET cc_start: 0.8271 (tpp) cc_final: 0.7768 (ttm) REVERT: I 34 MET cc_start: 0.0413 (mmt) cc_final: 0.0057 (mmt) REVERT: I 82 MET cc_start: -0.1480 (ptp) cc_final: -0.3045 (mmm) REVERT: I 118 THR cc_start: 0.2928 (OUTLIER) cc_final: 0.2366 (p) REVERT: I 129 SER cc_start: 0.0110 (OUTLIER) cc_final: -0.0531 (t) REVERT: I 199 ASN cc_start: 0.1461 (OUTLIER) cc_final: 0.0757 (t0) REVERT: M 188 LYS cc_start: 0.4290 (mtmm) cc_final: 0.4037 (mtmt) REVERT: N 49 TYR cc_start: 0.2091 (OUTLIER) cc_final: 0.0546 (m-10) REVERT: N 89 GLN cc_start: 0.1913 (OUTLIER) cc_final: 0.1318 (mm-40) outliers start: 209 outliers final: 140 residues processed: 413 average time/residue: 0.4156 time to fit residues: 296.7016 Evaluate side-chains 358 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 206 time to evaluate : 3.579 ------------------------------------------------------------------------------- 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 187 LYS Chi-restraints excluded: chain A residue 193 VAL 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 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 392 PHE Chi-restraints excluded: chain A residue 403 ARG 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 557 LYS 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 699 LEU 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 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 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 117 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 389 ASP 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 523 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 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR 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 83 VAL Chi-restraints excluded: chain C residue 113 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 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 242 LEU 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 318 PHE 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 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 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU 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 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 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 20 THR 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 129 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 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 91 LEU Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 117 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 195 THR 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 142 ARG Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 203 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 329 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 223 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 395 optimal weight: 30.0000 chunk 363 optimal weight: 7.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 422 ASN A 658 ASN A 675 GLN B 481 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.195287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.164734 restraints weight = 66661.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.161356 restraints weight = 109929.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158593 restraints weight = 113232.720| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35190 Z= 0.174 Angle : 0.757 13.657 48013 Z= 0.362 Chirality : 0.050 0.590 5628 Planarity : 0.005 0.064 6062 Dihedral : 7.736 59.196 6122 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.78 % Favored : 91.97 % Rotamer: Outliers : 5.00 % Allowed : 23.12 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 4244 helix: 0.88 (0.20), residues: 695 sheet: -0.13 (0.15), residues: 1214 loop : -2.20 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 436 HIS 0.004 0.001 HIS J 166 PHE 0.024 0.002 PHE I 102 TYR 0.026 0.002 TYR M 32 ARG 0.005 0.000 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 48) link_NAG-ASN : angle 3.73409 ( 144) link_BETA1-4 : bond 0.00524 ( 23) link_BETA1-4 : angle 2.24144 ( 69) hydrogen bonds : bond 0.04044 ( 1139) hydrogen bonds : angle 5.47406 ( 3183) SS BOND : bond 0.00434 ( 50) SS BOND : angle 1.83182 ( 100) covalent geometry : bond 0.00409 (35069) covalent geometry : angle 0.72120 (47700) *********************** 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 405 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 218 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1685 (ptt) cc_final: 0.1047 (mmm) REVERT: A 226 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7610 (mp) REVERT: A 308 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8707 (m) REVERT: A 460 ASN cc_start: 0.6948 (m-40) cc_final: 0.6557 (m-40) REVERT: A 1029 MET cc_start: 0.8932 (tpp) cc_final: 0.8730 (ttm) REVERT: B 189 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7262 (tp) REVERT: B 245 HIS cc_start: 0.3902 (OUTLIER) cc_final: 0.0670 (p-80) REVERT: B 266 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8517 (m-80) REVERT: B 389 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6506 (p0) REVERT: B 869 MET cc_start: 0.8469 (mtt) cc_final: 0.8187 (mtt) REVERT: B 878 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8800 (tt) REVERT: C 97 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.5961 (tttm) REVERT: C 266 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: C 796 ASP cc_start: 0.7400 (t0) cc_final: 0.7044 (p0) REVERT: C 1029 MET cc_start: 0.8205 (tpp) cc_final: 0.7787 (ttm) REVERT: I 82 MET cc_start: -0.1791 (ptp) cc_final: -0.3238 (mmm) REVERT: I 118 THR cc_start: 0.2900 (OUTLIER) cc_final: 0.2353 (p) REVERT: I 129 SER cc_start: 0.0271 (OUTLIER) cc_final: -0.0158 (t) REVERT: I 199 ASN cc_start: 0.1637 (OUTLIER) cc_final: 0.0856 (t0) REVERT: M 188 LYS cc_start: 0.4282 (mtmm) cc_final: 0.4054 (mtmt) REVERT: J 18 LEU cc_start: 0.1175 (tp) cc_final: 0.0617 (mp) REVERT: N 32 TYR cc_start: 0.2778 (OUTLIER) cc_final: 0.2459 (p90) REVERT: N 49 TYR cc_start: 0.1969 (OUTLIER) cc_final: 0.0534 (m-10) REVERT: N 89 GLN cc_start: 0.1836 (OUTLIER) cc_final: 0.1159 (tp40) REVERT: N 108 ARG cc_start: 0.1668 (OUTLIER) cc_final: 0.0689 (tmt170) outliers start: 187 outliers final: 135 residues processed: 383 average time/residue: 0.4160 time to fit residues: 271.9060 Evaluate side-chains 345 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 194 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 226 LEU 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 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 399 SER Chi-restraints excluded: chain A residue 403 ARG 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 560 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 699 LEU 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 882 ILE 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 1006 THR Chi-restraints excluded: chain A residue 1017 GLU 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 189 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 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 638 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET 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 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 83 VAL Chi-restraints excluded: chain C residue 97 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 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 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 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 745 ASP Chi-restraints excluded: chain C residue 753 LEU 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 922 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 950 ASP 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 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 92 VAL Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain K residue 20 THR 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 118 THR Chi-restraints excluded: chain I residue 129 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 185 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 199 ASN 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 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 126 LEU 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 108 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 354 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 320 optimal weight: 6.9990 chunk 402 optimal weight: 20.0000 chunk 267 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 81 ASN B 125 ASN B 334 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN C 536 ASN H 194 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN I 173 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 = 0.4403 r_free = 0.4403 target = 0.192655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.162098 restraints weight = 66464.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.158358 restraints weight = 110655.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155464 restraints weight = 113775.170| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.6607 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= 0.220 Angle : 0.810 14.388 48013 Z= 0.387 Chirality : 0.052 0.643 5628 Planarity : 0.005 0.064 6062 Dihedral : 8.010 59.259 6121 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.28 % Favored : 90.48 % Rotamer: Outliers : 5.67 % Allowed : 23.09 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 4244 helix: 0.78 (0.20), residues: 702 sheet: -0.23 (0.15), residues: 1221 loop : -2.25 (0.12), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 105 HIS 0.005 0.001 HIS A1064 PHE 0.028 0.002 PHE B 133 TYR 0.030 0.002 TYR B 904 ARG 0.006 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 48) link_NAG-ASN : angle 3.91608 ( 144) link_BETA1-4 : bond 0.00504 ( 23) link_BETA1-4 : angle 2.24452 ( 69) hydrogen bonds : bond 0.04529 ( 1139) hydrogen bonds : angle 5.62322 ( 3183) SS BOND : bond 0.00502 ( 50) SS BOND : angle 1.94614 ( 100) covalent geometry : bond 0.00525 (35069) covalent geometry : angle 0.77427 (47700) *********************** 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 431 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 219 time to evaluate : 3.329 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: 0.1847 (ptt) cc_final: 0.1368 (mmm) REVERT: A 205 SER cc_start: 0.8436 (m) cc_final: 0.7904 (p) REVERT: A 226 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7257 (mp) REVERT: A 308 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8748 (m) REVERT: A 460 ASN cc_start: 0.7085 (m-40) cc_final: 0.6625 (m-40) REVERT: A 1029 MET cc_start: 0.8502 (tpp) cc_final: 0.8255 (ttm) REVERT: B 189 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7345 (tp) REVERT: B 245 HIS cc_start: 0.3905 (OUTLIER) cc_final: 0.0707 (p-80) REVERT: B 389 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6753 (p0) REVERT: B 554 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: B 869 MET cc_start: 0.8510 (mtt) cc_final: 0.8191 (mtt) REVERT: B 878 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8633 (tt) REVERT: C 95 THR cc_start: 0.4777 (OUTLIER) cc_final: 0.4445 (t) REVERT: C 97 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.6198 (tttm) REVERT: C 266 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.6536 (m-80) REVERT: C 796 ASP cc_start: 0.7460 (t0) cc_final: 0.7223 (p0) REVERT: C 1021 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8675 (t) REVERT: C 1029 MET cc_start: 0.8667 (tpp) cc_final: 0.8407 (ttm) REVERT: H 3 GLN cc_start: 0.6511 (mp-120) cc_final: 0.5908 (tm-30) REVERT: I 82 MET cc_start: -0.1355 (ptp) cc_final: -0.2978 (mmm) REVERT: J 18 LEU cc_start: 0.1176 (tp) cc_final: 0.0773 (pp) REVERT: N 32 TYR cc_start: 0.2580 (OUTLIER) cc_final: 0.2153 (p90) REVERT: N 49 TYR cc_start: 0.1832 (OUTLIER) cc_final: 0.0298 (m-10) REVERT: N 89 GLN cc_start: 0.2023 (OUTLIER) cc_final: 0.1515 (mm-40) REVERT: N 108 ARG cc_start: 0.1926 (OUTLIER) cc_final: 0.0860 (tmt170) outliers start: 212 outliers final: 148 residues processed: 405 average time/residue: 0.5093 time to fit residues: 362.5301 Evaluate side-chains 358 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 195 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 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 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 403 ARG 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 553 THR Chi-restraints excluded: chain A residue 560 LEU 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 608 VAL Chi-restraints excluded: chain A residue 618 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 1006 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR 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 208 THR Chi-restraints excluded: chain B residue 214 ARG 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 293 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP 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 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 620 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 732 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 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 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 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 113 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 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 539 VAL Chi-restraints excluded: chain C residue 551 VAL 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 745 ASP Chi-restraints excluded: chain C residue 753 LEU 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 950 ASP 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 1100 THR 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 92 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 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 19 VAL Chi-restraints excluded: chain M residue 58 VAL 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 110 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 LEU 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 108 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 283 optimal weight: 8.9990 chunk 189 optimal weight: 0.8980 chunk 310 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 249 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 399 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 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** M 155 GLN J 157 ASN J 166 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.195701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.168395 restraints weight = 65970.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.164988 restraints weight = 107347.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.159963 restraints weight = 110765.227| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35190 Z= 0.131 Angle : 0.719 12.883 48013 Z= 0.342 Chirality : 0.049 0.539 5628 Planarity : 0.004 0.057 6062 Dihedral : 7.547 59.691 6119 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.19 % Favored : 92.60 % Rotamer: Outliers : 3.82 % Allowed : 24.85 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 4244 helix: 1.12 (0.20), residues: 702 sheet: -0.09 (0.15), residues: 1190 loop : -2.09 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 436 HIS 0.003 0.001 HIS J 202 PHE 0.025 0.001 PHE A 168 TYR 0.024 0.001 TYR M 32 ARG 0.012 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 48) link_NAG-ASN : angle 3.50879 ( 144) link_BETA1-4 : bond 0.00578 ( 23) link_BETA1-4 : angle 2.12695 ( 69) hydrogen bonds : bond 0.03698 ( 1139) hydrogen bonds : angle 5.35553 ( 3183) SS BOND : bond 0.00731 ( 50) SS BOND : angle 1.56317 ( 100) covalent geometry : bond 0.00296 (35069) covalent geometry : angle 0.68684 (47700) *********************** 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 362 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 219 time to evaluate : 3.400 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 153 MET cc_start: 0.1991 (ptt) cc_final: 0.1647 (mmm) REVERT: A 308 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8682 (m) REVERT: A 460 ASN cc_start: 0.7083 (m-40) cc_final: 0.6611 (m-40) REVERT: A 1029 MET cc_start: 0.8794 (tpp) cc_final: 0.8506 (ttm) REVERT: B 189 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7398 (tp) REVERT: B 245 HIS cc_start: 0.4162 (OUTLIER) cc_final: 0.0553 (p-80) REVERT: B 389 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6622 (p0) REVERT: B 554 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: B 869 MET cc_start: 0.8395 (mtt) cc_final: 0.8105 (mtt) REVERT: B 878 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8714 (tt) REVERT: C 95 THR cc_start: 0.4881 (OUTLIER) cc_final: 0.4521 (t) REVERT: C 266 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.6322 (m-80) REVERT: C 796 ASP cc_start: 0.7418 (t0) cc_final: 0.7118 (p0) REVERT: C 1029 MET cc_start: 0.8341 (tpp) cc_final: 0.8050 (ttm) REVERT: H 3 GLN cc_start: 0.6352 (mp-120) cc_final: 0.5848 (tm-30) REVERT: K 20 THR cc_start: 0.3229 (OUTLIER) cc_final: 0.2334 (t) REVERT: I 82 MET cc_start: -0.1401 (ptp) cc_final: -0.3067 (mmm) REVERT: J 18 LEU cc_start: 0.1239 (tp) cc_final: 0.0857 (pp) REVERT: N 32 TYR cc_start: 0.2245 (OUTLIER) cc_final: 0.1766 (p90) REVERT: N 49 TYR cc_start: 0.1267 (OUTLIER) cc_final: 0.0068 (m-10) REVERT: N 89 GLN cc_start: 0.2066 (OUTLIER) cc_final: 0.1627 (mm-40) REVERT: N 115 VAL cc_start: -0.1046 (OUTLIER) cc_final: -0.1354 (m) outliers start: 143 outliers final: 109 residues processed: 341 average time/residue: 0.4168 time to fit residues: 243.7674 Evaluate side-chains 326 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 204 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 114 THR 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 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 399 SER Chi-restraints excluded: chain A residue 403 ARG 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 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 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 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 208 THR 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 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 GLU 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 697 MET 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 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 968 SER Chi-restraints excluded: chain B residue 976 VAL 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 83 VAL Chi-restraints excluded: chain C residue 95 THR 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 242 LEU Chi-restraints excluded: chain C residue 266 TYR 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 753 LEU 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 948 LEU Chi-restraints excluded: chain C residue 950 ASP 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 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 92 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 20 THR 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 155 GLN 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 115 VAL Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 146 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 43 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 356 optimal weight: 40.0000 chunk 327 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 chunk 396 optimal weight: 50.0000 chunk 127 optimal weight: 20.0000 chunk 317 optimal weight: 50.0000 chunk 387 optimal weight: 40.0000 chunk 37 optimal weight: 20.0000 chunk 205 optimal weight: 3.9990 overall best weight: 8.9190 ------------------------------------------------------------------------------- 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 655 HIS B 134 GLN B 360 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 751 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 HIS ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.189286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158516 restraints weight = 66124.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155981 restraints weight = 111862.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.152665 restraints weight = 108593.250| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 35190 Z= 0.397 Angle : 0.999 15.676 48013 Z= 0.485 Chirality : 0.059 0.698 5628 Planarity : 0.006 0.065 6062 Dihedral : 8.880 59.626 6111 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.05 % Favored : 88.69 % Rotamer: Outliers : 4.84 % Allowed : 23.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.12), residues: 4244 helix: 0.26 (0.19), residues: 684 sheet: -0.52 (0.15), residues: 1183 loop : -2.48 (0.11), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 886 HIS 0.007 0.002 HIS A1064 PHE 0.042 0.003 PHE A 65 TYR 0.031 0.003 TYR I 33 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00862 ( 48) link_NAG-ASN : angle 4.37259 ( 144) link_BETA1-4 : bond 0.00578 ( 23) link_BETA1-4 : angle 2.51342 ( 69) hydrogen bonds : bond 0.05833 ( 1139) hydrogen bonds : angle 6.20519 ( 3183) SS BOND : bond 0.00624 ( 50) SS BOND : angle 2.30378 ( 100) covalent geometry : bond 0.00957 (35069) covalent geometry : angle 0.96243 (47700) *********************** 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 374 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 193 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1653 (ptt) cc_final: 0.1450 (mmm) REVERT: A 205 SER cc_start: 0.8588 (m) cc_final: 0.8195 (p) REVERT: A 226 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7239 (mp) REVERT: A 308 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8827 (m) REVERT: A 360 ASN cc_start: 0.5745 (OUTLIER) cc_final: 0.5096 (p0) REVERT: A 460 ASN cc_start: 0.6963 (m-40) cc_final: 0.6520 (m-40) REVERT: A 998 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8482 (p) REVERT: B 52 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6835 (tp40) REVERT: B 189 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7616 (tp) REVERT: B 245 HIS cc_start: 0.4314 (OUTLIER) cc_final: 0.1231 (p90) REVERT: B 389 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7045 (p0) REVERT: B 554 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: B 869 MET cc_start: 0.8539 (mtt) cc_final: 0.8243 (mtt) REVERT: B 902 MET cc_start: 0.8784 (mmt) cc_final: 0.8515 (tpt) REVERT: C 190 ARG cc_start: 0.6984 (mmt180) cc_final: 0.6343 (mmm-85) REVERT: C 266 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.6747 (m-80) REVERT: C 355 ARG cc_start: 0.6099 (ttt180) cc_final: 0.5730 (tpp-160) REVERT: C 1021 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8857 (t) REVERT: C 1029 MET cc_start: 0.8619 (tpp) cc_final: 0.8353 (ttm) REVERT: H 3 GLN cc_start: 0.6699 (mp-120) cc_final: 0.5806 (tm-30) REVERT: I 82 MET cc_start: -0.1287 (ptp) cc_final: -0.2950 (mmm) REVERT: I 103 ASP cc_start: 0.5899 (OUTLIER) cc_final: 0.4800 (t0) REVERT: M 91 LEU cc_start: 0.2942 (OUTLIER) cc_final: 0.2316 (pp) REVERT: J 18 LEU cc_start: 0.1991 (tp) cc_final: 0.1077 (pp) REVERT: N 49 TYR cc_start: 0.1708 (OUTLIER) cc_final: 0.0508 (m-10) REVERT: N 89 GLN cc_start: 0.2695 (OUTLIER) cc_final: 0.2261 (mm-40) REVERT: N 108 ARG cc_start: 0.2216 (OUTLIER) cc_final: 0.0914 (tmt170) REVERT: N 115 VAL cc_start: -0.1475 (OUTLIER) cc_final: -0.1734 (m) outliers start: 181 outliers final: 130 residues processed: 354 average time/residue: 0.4597 time to fit residues: 283.2032 Evaluate side-chains 328 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 181 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 193 VAL 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 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 360 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 403 ARG 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 560 LEU 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 608 VAL Chi-restraints excluded: chain A residue 618 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 813 SER Chi-restraints excluded: chain A residue 859 THR 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 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR 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 293 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP 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 503 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 554 GLU 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 620 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 791 THR 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 976 VAL 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 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 141 LEU 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 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 539 VAL 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 620 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 753 LEU 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 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 1100 THR 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 92 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 58 VAL 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 110 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 102 PHE 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 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 115 VAL 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 183 optimal weight: 0.0010 chunk 416 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 356 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 322 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 312 optimal weight: 6.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 487 ASN A1106 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C1002 GLN ** 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** J 166 HIS ** J 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.193843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.164940 restraints weight = 65579.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.161892 restraints weight = 116998.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.159266 restraints weight = 110274.293| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.7284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35190 Z= 0.134 Angle : 0.750 13.096 48013 Z= 0.359 Chirality : 0.050 0.539 5628 Planarity : 0.005 0.101 6062 Dihedral : 7.786 59.949 6111 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.40 % Favored : 92.41 % Rotamer: Outliers : 2.94 % Allowed : 25.84 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 4244 helix: 0.97 (0.20), residues: 693 sheet: -0.25 (0.15), residues: 1167 loop : -2.22 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 436 HIS 0.004 0.001 HIS M 189 PHE 0.030 0.002 PHE A 238 TYR 0.025 0.001 TYR M 32 ARG 0.032 0.001 ARG N 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 48) link_NAG-ASN : angle 3.53150 ( 144) link_BETA1-4 : bond 0.00543 ( 23) link_BETA1-4 : angle 2.16308 ( 69) hydrogen bonds : bond 0.03881 ( 1139) hydrogen bonds : angle 5.53214 ( 3183) SS BOND : bond 0.00423 ( 50) SS BOND : angle 1.66525 ( 100) covalent geometry : bond 0.00298 (35069) covalent geometry : angle 0.71882 (47700) ********************** 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 320 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 210 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8759 (m) REVERT: A 460 ASN cc_start: 0.7091 (m-40) cc_final: 0.6653 (m-40) REVERT: A 1029 MET cc_start: 0.8506 (tpp) cc_final: 0.8232 (ttm) REVERT: B 245 HIS cc_start: 0.4343 (OUTLIER) cc_final: 0.0734 (p-80) REVERT: B 389 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6755 (p0) REVERT: B 554 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: B 869 MET cc_start: 0.8400 (mtt) cc_final: 0.8120 (mtt) REVERT: B 878 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8827 (tt) REVERT: C 190 ARG cc_start: 0.6834 (mmt180) cc_final: 0.6360 (mmm-85) REVERT: C 266 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: C 1029 MET cc_start: 0.8316 (tpp) cc_final: 0.7885 (ttm) REVERT: H 3 GLN cc_start: 0.6446 (mp-120) cc_final: 0.5738 (tm-30) REVERT: H 82 MET cc_start: 0.1044 (mtm) cc_final: 0.0649 (ptp) REVERT: K 20 THR cc_start: 0.3338 (OUTLIER) cc_final: 0.2430 (t) REVERT: I 82 MET cc_start: -0.1522 (ptp) cc_final: -0.3388 (mmm) REVERT: M 91 LEU cc_start: 0.2795 (OUTLIER) cc_final: 0.2318 (pp) REVERT: J 18 LEU cc_start: 0.1879 (tp) cc_final: 0.1146 (pp) REVERT: N 49 TYR cc_start: 0.1424 (OUTLIER) cc_final: 0.0363 (m-10) REVERT: N 89 GLN cc_start: 0.2496 (OUTLIER) cc_final: 0.1857 (mm-40) REVERT: N 90 GLN cc_start: 0.1098 (OUTLIER) cc_final: 0.0339 (mt0) REVERT: N 108 ARG cc_start: 0.2229 (OUTLIER) cc_final: 0.1558 (tmt170) REVERT: N 115 VAL cc_start: -0.1363 (OUTLIER) cc_final: -0.1632 (m) outliers start: 110 outliers final: 79 residues processed: 307 average time/residue: 0.5951 time to fit residues: 319.7533 Evaluate side-chains 290 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 198 time to evaluate : 4.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 236 THR 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 407 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 937 SER 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 208 THR 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 382 VAL Chi-restraints excluded: chain B residue 389 ASP 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 503 VAL Chi-restraints excluded: chain B residue 554 GLU 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 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU 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 83 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 242 LEU Chi-restraints excluded: chain C residue 266 TYR 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 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 856 ASN 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 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 92 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER 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 I residue 113 VAL Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain J residue 2 VAL 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 49 TYR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 115 VAL 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 304 optimal weight: 0.0970 chunk 256 optimal weight: 0.4980 chunk 423 optimal weight: 20.0000 chunk 413 optimal weight: 8.9990 chunk 322 optimal weight: 8.9990 chunk 384 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 74 optimal weight: 0.3980 chunk 310 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN C 196 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.193744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.165569 restraints weight = 66015.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.161747 restraints weight = 114722.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.158543 restraints weight = 113885.643| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.7350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35190 Z= 0.139 Angle : 0.739 12.635 48013 Z= 0.353 Chirality : 0.049 0.553 5628 Planarity : 0.005 0.083 6062 Dihedral : 7.515 59.569 6111 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.77 % Favored : 91.05 % Rotamer: Outliers : 3.15 % Allowed : 25.79 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 4244 helix: 1.13 (0.20), residues: 699 sheet: -0.17 (0.15), residues: 1157 loop : -2.16 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 PHE 0.045 0.002 PHE C 65 TYR 0.026 0.001 TYR B 904 ARG 0.021 0.000 ARG N 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 48) link_NAG-ASN : angle 3.37398 ( 144) link_BETA1-4 : bond 0.00552 ( 23) link_BETA1-4 : angle 2.08541 ( 69) hydrogen bonds : bond 0.03809 ( 1139) hydrogen bonds : angle 5.37473 ( 3183) SS BOND : bond 0.00458 ( 50) SS BOND : angle 1.90219 ( 100) covalent geometry : bond 0.00319 (35069) covalent geometry : angle 0.70856 (47700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11520.86 seconds wall clock time: 207 minutes 16.28 seconds (12436.28 seconds total)