Starting phenix.real_space_refine on Fri Jan 16 00:08:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y9z_33697/01_2026/7y9z_33697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y9z_33697/01_2026/7y9z_33697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y9z_33697/01_2026/7y9z_33697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y9z_33697/01_2026/7y9z_33697.map" model { file = "/net/cci-nas-00/data/ceres_data/7y9z_33697/01_2026/7y9z_33697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y9z_33697/01_2026/7y9z_33697.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 143 5.16 5 C 19681 2.51 5 N 5047 2.21 5 O 5965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30837 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8336 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 59, 'TRANS': 1002} Chain breaks: 7 Chain: "B" Number of atoms: 8357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8357 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 59, 'TRANS': 1005} Chain breaks: 7 Chain: "C" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8336 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 59, 'TRANS': 1002} Chain breaks: 7 Chain: "D" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.40, per 1000 atoms: 0.24 Number of scatterers: 30837 At special positions: 0 Unit cell: (140.58, 147.84, 246.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 143 16.00 O 5965 8.00 N 5047 7.00 C 19681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.03 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.06 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 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-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 616 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 343 " " NAG B1309 " - " ASN B 616 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 709 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 374 " 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7130 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 47 sheets defined 30.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.643A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.919A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.577A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.804A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.685A pdb=" N ASN A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.779A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.683A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.504A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.162A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.578A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.739A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.521A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.580A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 746 through 751' Processing helix chain 'B' and resid 752 through 757 removed outlier: 3.581A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.552A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.236A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.631A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.524A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.961A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.077A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.559A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.910A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.518A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.165A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.031A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 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 976 through 984 removed outlier: 3.656A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.906A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.063A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 4.228A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 92 through 102 removed outlier: 4.182A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.870A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.217A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.762A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 removed outlier: 3.705A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.542A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 4.120A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 413 removed outlier: 5.669A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.638A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.554A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.621A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.748A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.117A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.596A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.509A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.549A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.311A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.300A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.098A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.587A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.536A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 4.338A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.768A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.340A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.611A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.868A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.752A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.640A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 133 through 142 removed outlier: 8.886A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.958A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.012A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.879A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.890A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 567 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.960A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.820A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.820A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.654A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.987A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.555A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.722A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.471A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.243A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.250A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.737A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.737A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.585A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AF1, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.939A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 347 through 350 1299 hydrogen bonds defined for protein. 3605 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: 6.86 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8271 1.33 - 1.46: 8445 1.46 - 1.58: 14665 1.58 - 1.71: 0 1.71 - 1.84: 191 Bond restraints: 31572 Sorted by residual: bond pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 1.473 1.416 0.057 1.32e-02 5.74e+03 1.86e+01 bond pdb=" N CYS B 617 " pdb=" CA CYS B 617 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.70e+00 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.455 1.477 -0.022 7.00e-03 2.04e+04 9.44e+00 bond pdb=" N CYS A 617 " pdb=" CA CYS A 617 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.10e+00 bond pdb=" N CYS C 538 " pdb=" CA CYS C 538 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 7.89e+00 ... (remaining 31567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 42357 2.61 - 5.23: 551 5.23 - 7.84: 41 7.84 - 10.46: 6 10.46 - 13.07: 3 Bond angle restraints: 42958 Sorted by residual: angle pdb=" N PRO A 384 " pdb=" CA PRO A 384 " pdb=" C PRO A 384 " ideal model delta sigma weight residual 113.47 101.84 11.63 1.43e+00 4.89e-01 6.61e+01 angle pdb=" N ALA D 403 " pdb=" CA ALA D 403 " pdb=" C ALA D 403 " ideal model delta sigma weight residual 110.80 97.73 13.07 2.13e+00 2.20e-01 3.77e+01 angle pdb=" C THR C 376 " pdb=" N PHE C 377 " pdb=" CA PHE C 377 " ideal model delta sigma weight residual 121.54 110.73 10.81 1.91e+00 2.74e-01 3.20e+01 angle pdb=" C GLU D 402 " pdb=" CA GLU D 402 " pdb=" CB GLU D 402 " ideal model delta sigma weight residual 111.41 102.32 9.09 1.65e+00 3.67e-01 3.03e+01 angle pdb=" CA CYS C 391 " pdb=" C CYS C 391 " pdb=" O CYS C 391 " ideal model delta sigma weight residual 121.87 115.95 5.92 1.16e+00 7.43e-01 2.60e+01 ... (remaining 42953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 17839 17.66 - 35.32: 1440 35.32 - 52.97: 303 52.97 - 70.63: 72 70.63 - 88.29: 39 Dihedral angle restraints: 19693 sinusoidal: 8632 harmonic: 11061 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 176.30 -83.30 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -3.71 -82.29 1 1.00e+01 1.00e-02 8.31e+01 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 93.00 171.27 -78.27 1 1.00e+01 1.00e-02 7.65e+01 ... (remaining 19690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 4991 0.261 - 0.521: 7 0.521 - 0.782: 0 0.782 - 1.042: 0 1.042 - 1.303: 1 Chirality restraints: 4999 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.24e+01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 4996 not shown) Planarity restraints: 5506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 378 " 0.025 2.00e-02 2.50e+03 5.24e-02 2.74e+01 pdb=" C LYS A 378 " -0.091 2.00e-02 2.50e+03 pdb=" O LYS A 378 " 0.035 2.00e-02 2.50e+03 pdb=" N CYS A 379 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.044 2.00e-02 2.50e+03 4.31e-02 2.32e+01 pdb=" CG ASN A 234 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.054 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " -0.078 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO C 337 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " -0.063 5.00e-02 4.00e+02 ... (remaining 5503 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1328 2.72 - 3.27: 30113 3.27 - 3.81: 47990 3.81 - 4.36: 57239 4.36 - 4.90: 100139 Nonbonded interactions: 236809 Sorted by model distance: nonbonded pdb=" O ASN A 388 " pdb=" OD1 ASP A 389 " model vdw 2.175 3.040 nonbonded pdb=" OG SER D 77 " pdb=" O GLN D 101 " model vdw 2.200 3.040 nonbonded pdb=" NZ LYS A 535 " pdb=" OE2 GLU A 554 " model vdw 2.204 3.120 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OD1 ASN C 394 " model vdw 2.219 3.040 ... (remaining 236804 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' selection = (chain 'B' and (resid 14 through 827 or resid 848 through 1306)) selection = (chain 'C' and resid 14 through 1306) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' 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' } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.800 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 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 : 0.005 0.209 31686 Z= 0.224 Angle : 0.739 15.944 43249 Z= 0.392 Chirality : 0.053 1.303 4999 Planarity : 0.006 0.120 5461 Dihedral : 13.629 88.290 12428 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.78 % Favored : 93.84 % Rotamer: Outliers : 0.45 % Allowed : 0.45 % Favored : 99.10 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3736 helix: 1.34 (0.17), residues: 1032 sheet: 0.83 (0.19), residues: 682 loop : -1.52 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.037 0.001 TYR A 453 PHE 0.022 0.001 PHE D 327 TRP 0.028 0.002 TRP D 461 HIS 0.031 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00438 (31572) covalent geometry : angle 0.70516 (42958) SS BOND : bond 0.00604 ( 45) SS BOND : angle 2.35573 ( 90) hydrogen bonds : bond 0.12823 ( 1263) hydrogen bonds : angle 5.97126 ( 3605) metal coordination : bond 0.17103 ( 2) link_BETA1-4 : bond 0.00679 ( 22) link_BETA1-4 : angle 2.16606 ( 66) link_NAG-ASN : bond 0.00427 ( 45) link_NAG-ASN : angle 3.26537 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 672 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8184 (mptt) cc_final: 0.7892 (mptt) REVERT: A 364 ASP cc_start: 0.7502 (p0) cc_final: 0.7137 (p0) REVERT: A 405 ASP cc_start: 0.7144 (t0) cc_final: 0.6772 (t0) REVERT: A 406 GLU cc_start: 0.7506 (pt0) cc_final: 0.7028 (pt0) REVERT: A 528 LYS cc_start: 0.7523 (mmpt) cc_final: 0.7295 (mmpt) REVERT: B 855 PHE cc_start: 0.8485 (m-10) cc_final: 0.8275 (m-80) REVERT: B 1084 ASP cc_start: 0.6660 (t70) cc_final: 0.6319 (t0) REVERT: C 121 ASN cc_start: 0.7368 (t0) cc_final: 0.7116 (t0) REVERT: C 206 LYS cc_start: 0.8084 (tptp) cc_final: 0.7829 (tmtm) REVERT: C 424 LYS cc_start: 0.8245 (tttp) cc_final: 0.8027 (ttmm) REVERT: C 465 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6351 (tm-30) REVERT: C 776 LYS cc_start: 0.8069 (tttm) cc_final: 0.7834 (ttpp) REVERT: C 1045 LYS cc_start: 0.7714 (tppt) cc_final: 0.7299 (tppt) REVERT: C 1084 ASP cc_start: 0.7306 (t0) cc_final: 0.6970 (t0) REVERT: D 34 HIS cc_start: 0.7272 (t-90) cc_final: 0.6868 (t-90) REVERT: D 41 TYR cc_start: 0.7270 (t80) cc_final: 0.7059 (t80) REVERT: D 42 GLN cc_start: 0.7968 (pm20) cc_final: 0.7128 (mp10) REVERT: D 57 GLU cc_start: 0.7041 (pm20) cc_final: 0.6701 (pm20) REVERT: D 60 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7839 (tm-30) REVERT: D 199 TYR cc_start: 0.4076 (t80) cc_final: 0.3395 (t80) REVERT: D 309 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7108 (mmtm) REVERT: D 375 GLU cc_start: 0.6126 (pm20) cc_final: 0.5273 (tt0) REVERT: D 380 GLN cc_start: 0.7206 (mp-120) cc_final: 0.6632 (mp-120) outliers start: 15 outliers final: 6 residues processed: 684 average time/residue: 0.6021 time to fit residues: 489.2620 Evaluate side-chains 620 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 614 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 675 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 196 ASN A 239 GLN A 321 GLN A 388 ASN A 755 GLN A 907 ASN A1005 GLN B 606 ASN B 960 ASN B1010 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 606 ASN C1010 GLN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.183245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135023 restraints weight = 62097.344| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.58 r_work: 0.3520 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 31686 Z= 0.189 Angle : 0.685 12.613 43249 Z= 0.342 Chirality : 0.048 0.438 4999 Planarity : 0.006 0.091 5461 Dihedral : 7.887 59.669 5484 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.68 % Favored : 94.14 % Rotamer: Outliers : 1.86 % Allowed : 9.05 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3736 helix: 1.31 (0.17), residues: 1035 sheet: 0.90 (0.19), residues: 688 loop : -1.50 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 403 TYR 0.035 0.002 TYR A 495 PHE 0.024 0.002 PHE D 327 TRP 0.020 0.002 TRP D 203 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00448 (31572) covalent geometry : angle 0.65555 (42958) SS BOND : bond 0.00386 ( 45) SS BOND : angle 1.98826 ( 90) hydrogen bonds : bond 0.05673 ( 1263) hydrogen bonds : angle 5.20892 ( 3605) metal coordination : bond 0.01045 ( 2) link_BETA1-4 : bond 0.00727 ( 22) link_BETA1-4 : angle 1.80314 ( 66) link_NAG-ASN : bond 0.00378 ( 45) link_NAG-ASN : angle 3.02918 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 626 time to evaluate : 1.092 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 113 LYS cc_start: 0.8339 (mptt) cc_final: 0.8006 (mptt) REVERT: A 364 ASP cc_start: 0.7979 (p0) cc_final: 0.7557 (p0) REVERT: A 405 ASP cc_start: 0.7721 (t0) cc_final: 0.7329 (t0) REVERT: A 450 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8302 (t0) REVERT: A 528 LYS cc_start: 0.7908 (mmpt) cc_final: 0.7657 (mmpt) REVERT: A 539 VAL cc_start: 0.8455 (t) cc_final: 0.8169 (m) REVERT: A 988 GLU cc_start: 0.7982 (tp30) cc_final: 0.7758 (mm-30) REVERT: B 121 ASN cc_start: 0.7085 (t0) cc_final: 0.6749 (t0) REVERT: B 304 LYS cc_start: 0.8560 (tppt) cc_final: 0.8355 (mptt) REVERT: B 576 VAL cc_start: 0.7519 (t) cc_final: 0.7231 (p) REVERT: B 780 GLU cc_start: 0.7734 (pp20) cc_final: 0.7478 (pp20) REVERT: B 825 LYS cc_start: 0.8117 (mmmm) cc_final: 0.7792 (mtpp) REVERT: B 1072 GLU cc_start: 0.8293 (pm20) cc_final: 0.8084 (pm20) REVERT: B 1084 ASP cc_start: 0.7464 (t70) cc_final: 0.7042 (t0) REVERT: C 465 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6963 (tm-30) REVERT: C 558 LYS cc_start: 0.8759 (mppt) cc_final: 0.8528 (mppt) REVERT: C 776 LYS cc_start: 0.8733 (tttm) cc_final: 0.8475 (ttpp) REVERT: C 820 ASP cc_start: 0.7986 (m-30) cc_final: 0.7721 (m-30) REVERT: C 1045 LYS cc_start: 0.8322 (tppt) cc_final: 0.7922 (tppt) REVERT: C 1084 ASP cc_start: 0.7923 (t0) cc_final: 0.7447 (t0) REVERT: D 34 HIS cc_start: 0.7512 (t-90) cc_final: 0.7131 (t-90) REVERT: D 41 TYR cc_start: 0.7366 (t80) cc_final: 0.7040 (t80) REVERT: D 42 GLN cc_start: 0.7985 (pm20) cc_final: 0.7252 (mp10) REVERT: D 48 TRP cc_start: 0.7194 (t-100) cc_final: 0.6910 (t-100) REVERT: D 57 GLU cc_start: 0.7261 (pm20) cc_final: 0.7044 (pm20) REVERT: D 60 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7924 (tm-30) REVERT: D 68 LYS cc_start: 0.8258 (mptp) cc_final: 0.7916 (mmtm) REVERT: D 199 TYR cc_start: 0.4351 (t80) cc_final: 0.3521 (t80) REVERT: D 309 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7081 (mmtm) REVERT: D 330 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.7033 (t0) REVERT: D 341 LYS cc_start: 0.6947 (mmmt) cc_final: 0.6548 (mmmt) REVERT: D 435 GLU cc_start: 0.5189 (tp30) cc_final: 0.4481 (tt0) REVERT: D 455 MET cc_start: 0.6400 (mmt) cc_final: 0.6057 (tpt) REVERT: D 526 GLN cc_start: 0.7525 (mp10) cc_final: 0.7148 (mp10) REVERT: D 579 MET cc_start: 0.1143 (tpt) cc_final: -0.1180 (ttp) outliers start: 62 outliers final: 26 residues processed: 649 average time/residue: 0.6103 time to fit residues: 470.2678 Evaluate side-chains 650 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 622 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 376 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 310 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 294 optimal weight: 0.9990 chunk 342 optimal weight: 50.0000 chunk 277 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 603 ASN A 755 GLN A 907 ASN A1005 GLN B 196 ASN B 606 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 532 ASN C 628 GLN C1010 GLN D 63 ASN D 330 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.182874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134678 restraints weight = 62466.625| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.56 r_work: 0.3523 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31686 Z= 0.182 Angle : 0.663 10.680 43249 Z= 0.332 Chirality : 0.047 0.301 4999 Planarity : 0.005 0.077 5461 Dihedral : 7.356 59.808 5476 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.56 % Rotamer: Outliers : 2.01 % Allowed : 11.60 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3736 helix: 1.35 (0.17), residues: 1035 sheet: 0.95 (0.19), residues: 678 loop : -1.48 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 403 TYR 0.030 0.002 TYR A 453 PHE 0.020 0.002 PHE D 315 TRP 0.018 0.001 TRP D 271 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00432 (31572) covalent geometry : angle 0.63558 (42958) SS BOND : bond 0.00545 ( 45) SS BOND : angle 1.86953 ( 90) hydrogen bonds : bond 0.05493 ( 1263) hydrogen bonds : angle 5.06428 ( 3605) metal coordination : bond 0.00244 ( 2) link_BETA1-4 : bond 0.00686 ( 22) link_BETA1-4 : angle 1.79867 ( 66) link_NAG-ASN : bond 0.00371 ( 45) link_NAG-ASN : angle 2.86441 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 637 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8337 (mptt) cc_final: 0.7990 (mptt) REVERT: A 129 LYS cc_start: 0.8564 (pttp) cc_final: 0.8292 (tmmm) REVERT: A 202 LYS cc_start: 0.8188 (mptt) cc_final: 0.7964 (mptt) REVERT: A 290 ASP cc_start: 0.8137 (t0) cc_final: 0.7931 (t0) REVERT: A 356 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8174 (ttpp) REVERT: A 364 ASP cc_start: 0.7968 (p0) cc_final: 0.7568 (p0) REVERT: A 378 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7061 (tmmt) REVERT: A 405 ASP cc_start: 0.7790 (t0) cc_final: 0.7377 (t0) REVERT: A 516 GLU cc_start: 0.6454 (tp30) cc_final: 0.6134 (tp30) REVERT: A 528 LYS cc_start: 0.7936 (mmpt) cc_final: 0.7693 (mmpt) REVERT: A 776 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8409 (tttp) REVERT: B 52 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: B 121 ASN cc_start: 0.7072 (t0) cc_final: 0.6776 (t0) REVERT: B 304 LYS cc_start: 0.8572 (tppt) cc_final: 0.8370 (mptt) REVERT: B 558 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7728 (mmtp) REVERT: B 576 VAL cc_start: 0.7486 (t) cc_final: 0.7176 (p) REVERT: B 673 SER cc_start: 0.8696 (t) cc_final: 0.8338 (p) REVERT: B 825 LYS cc_start: 0.8159 (mmmm) cc_final: 0.7862 (mtpp) REVERT: B 855 PHE cc_start: 0.8540 (m-80) cc_final: 0.8262 (m-80) REVERT: B 1084 ASP cc_start: 0.7464 (t70) cc_final: 0.6997 (t0) REVERT: C 343 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7504 (p0) REVERT: C 351 TYR cc_start: 0.8172 (p90) cc_final: 0.7853 (p90) REVERT: C 465 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6971 (tm-30) REVERT: C 558 LYS cc_start: 0.8717 (mppt) cc_final: 0.8499 (mppt) REVERT: C 776 LYS cc_start: 0.8709 (tttm) cc_final: 0.8474 (ttpp) REVERT: C 820 ASP cc_start: 0.8010 (m-30) cc_final: 0.7739 (m-30) REVERT: C 1045 LYS cc_start: 0.8349 (tppt) cc_final: 0.7966 (tppt) REVERT: C 1084 ASP cc_start: 0.7930 (t0) cc_final: 0.7438 (t0) REVERT: D 34 HIS cc_start: 0.7484 (t-90) cc_final: 0.7126 (t-90) REVERT: D 41 TYR cc_start: 0.7366 (t80) cc_final: 0.6954 (t80) REVERT: D 42 GLN cc_start: 0.8043 (pm20) cc_final: 0.7234 (mp10) REVERT: D 54 ILE cc_start: 0.7088 (pp) cc_final: 0.6746 (mp) REVERT: D 57 GLU cc_start: 0.7204 (pm20) cc_final: 0.7000 (pm20) REVERT: D 60 GLN cc_start: 0.8248 (tm-30) cc_final: 0.8018 (tm-30) REVERT: D 68 LYS cc_start: 0.8287 (mptp) cc_final: 0.8061 (mptp) REVERT: D 97 LEU cc_start: 0.7015 (mt) cc_final: 0.6759 (tp) REVERT: D 199 TYR cc_start: 0.4402 (t80) cc_final: 0.3210 (t80) REVERT: D 203 TRP cc_start: 0.3593 (m-10) cc_final: 0.0645 (m-90) REVERT: D 330 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7116 (t0) REVERT: D 435 GLU cc_start: 0.5149 (tp30) cc_final: 0.4483 (tt0) REVERT: D 524 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6441 (tt0) REVERT: D 579 MET cc_start: 0.1226 (tpt) cc_final: -0.0986 (ttp) outliers start: 67 outliers final: 35 residues processed: 665 average time/residue: 0.6089 time to fit residues: 481.3598 Evaluate side-chains 656 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 614 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 524 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 1.9990 chunk 150 optimal weight: 50.0000 chunk 353 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 351 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 363 optimal weight: 0.0470 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 755 GLN A1005 GLN B 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 603 ASN C1010 GLN D 103 ASN D 330 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.181318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135709 restraints weight = 54912.736| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.32 r_work: 0.3540 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31686 Z= 0.222 Angle : 0.676 9.806 43249 Z= 0.340 Chirality : 0.048 0.316 4999 Planarity : 0.005 0.074 5461 Dihedral : 7.099 58.779 5476 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 2.98 % Allowed : 13.10 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 3736 helix: 1.31 (0.17), residues: 1042 sheet: 0.89 (0.19), residues: 670 loop : -1.50 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 403 TYR 0.031 0.002 TYR B 265 PHE 0.023 0.002 PHE D 452 TRP 0.033 0.002 TRP D 48 HIS 0.006 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00533 (31572) covalent geometry : angle 0.64946 (42958) SS BOND : bond 0.00427 ( 45) SS BOND : angle 1.89491 ( 90) hydrogen bonds : bond 0.05800 ( 1263) hydrogen bonds : angle 5.06345 ( 3605) metal coordination : bond 0.00282 ( 2) link_BETA1-4 : bond 0.00667 ( 22) link_BETA1-4 : angle 1.81714 ( 66) link_NAG-ASN : bond 0.00380 ( 45) link_NAG-ASN : angle 2.84874 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 634 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8352 (mptt) cc_final: 0.8004 (mptt) REVERT: A 129 LYS cc_start: 0.8528 (pttp) cc_final: 0.8286 (tmmm) REVERT: A 356 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8167 (ttpp) REVERT: A 364 ASP cc_start: 0.7898 (p0) cc_final: 0.7602 (p0) REVERT: A 392 PHE cc_start: 0.8874 (m-80) cc_final: 0.8578 (m-80) REVERT: A 405 ASP cc_start: 0.7825 (t0) cc_final: 0.7417 (t0) REVERT: A 406 GLU cc_start: 0.7986 (pt0) cc_final: 0.7764 (pt0) REVERT: A 516 GLU cc_start: 0.6513 (tp30) cc_final: 0.6234 (tp30) REVERT: A 528 LYS cc_start: 0.7925 (mmpt) cc_final: 0.7696 (mmpt) REVERT: B 52 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: B 121 ASN cc_start: 0.7040 (t0) cc_final: 0.6694 (t0) REVERT: B 304 LYS cc_start: 0.8546 (tppt) cc_final: 0.8336 (mptt) REVERT: B 532 ASN cc_start: 0.7963 (t0) cc_final: 0.7696 (t0) REVERT: B 558 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7738 (mmtp) REVERT: B 576 VAL cc_start: 0.7507 (t) cc_final: 0.7203 (p) REVERT: B 673 SER cc_start: 0.8684 (t) cc_final: 0.8329 (p) REVERT: B 740 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8129 (ttt) REVERT: B 787 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: B 814 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7853 (ptpp) REVERT: B 825 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7946 (mtpp) REVERT: B 855 PHE cc_start: 0.8606 (m-80) cc_final: 0.8388 (m-80) REVERT: B 1072 GLU cc_start: 0.8221 (pm20) cc_final: 0.8004 (pm20) REVERT: B 1084 ASP cc_start: 0.7406 (t70) cc_final: 0.6916 (t0) REVERT: C 343 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7511 (p0) REVERT: C 351 TYR cc_start: 0.8190 (p90) cc_final: 0.7813 (p90) REVERT: C 465 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6900 (tm-30) REVERT: C 558 LYS cc_start: 0.8669 (mppt) cc_final: 0.8442 (mppt) REVERT: C 635 VAL cc_start: 0.5645 (OUTLIER) cc_final: 0.5358 (m) REVERT: C 646 ARG cc_start: 0.8053 (ttt-90) cc_final: 0.7727 (ttt-90) REVERT: C 776 LYS cc_start: 0.8696 (tttm) cc_final: 0.8463 (ttpp) REVERT: C 820 ASP cc_start: 0.7983 (m-30) cc_final: 0.7708 (m-30) REVERT: C 1045 LYS cc_start: 0.8313 (tppt) cc_final: 0.7929 (tppt) REVERT: C 1084 ASP cc_start: 0.7874 (t0) cc_final: 0.7405 (t0) REVERT: D 34 HIS cc_start: 0.7493 (t-90) cc_final: 0.7147 (t-90) REVERT: D 41 TYR cc_start: 0.7295 (t80) cc_final: 0.6930 (t80) REVERT: D 42 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: D 54 ILE cc_start: 0.7026 (pp) cc_final: 0.6705 (mp) REVERT: D 55 THR cc_start: 0.4129 (p) cc_final: 0.2906 (m) REVERT: D 57 GLU cc_start: 0.7177 (pm20) cc_final: 0.6781 (pm20) REVERT: D 60 GLN cc_start: 0.8212 (tm-30) cc_final: 0.8000 (tm-30) REVERT: D 68 LYS cc_start: 0.8290 (mptp) cc_final: 0.8053 (mmtm) REVERT: D 97 LEU cc_start: 0.7044 (mt) cc_final: 0.6789 (tp) REVERT: D 199 TYR cc_start: 0.4577 (t80) cc_final: 0.3348 (t80) REVERT: D 203 TRP cc_start: 0.3652 (m-10) cc_final: 0.0648 (m-90) REVERT: D 309 LYS cc_start: 0.7652 (mmtt) cc_final: 0.6955 (mmtm) REVERT: D 330 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.6950 (t0) REVERT: D 375 GLU cc_start: 0.5609 (OUTLIER) cc_final: 0.5409 (pm20) REVERT: D 435 GLU cc_start: 0.5208 (tp30) cc_final: 0.4568 (tt0) REVERT: D 524 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6402 (tt0) REVERT: D 579 MET cc_start: 0.1190 (tpt) cc_final: -0.0979 (ttp) outliers start: 99 outliers final: 52 residues processed: 679 average time/residue: 0.6020 time to fit residues: 489.9309 Evaluate side-chains 689 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 625 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 524 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 54 optimal weight: 0.6980 chunk 230 optimal weight: 0.5980 chunk 326 optimal weight: 10.0000 chunk 229 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 295 optimal weight: 0.6980 chunk 282 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 755 GLN A1005 GLN A1071 GLN B 196 ASN B 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 603 ASN C1010 GLN D 330 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.182368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135861 restraints weight = 51881.682| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.89 r_work: 0.3569 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31686 Z= 0.153 Angle : 0.649 9.592 43249 Z= 0.324 Chirality : 0.046 0.341 4999 Planarity : 0.005 0.073 5461 Dihedral : 6.817 59.336 5472 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.11 % Favored : 94.73 % Rotamer: Outliers : 2.68 % Allowed : 14.37 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3736 helix: 1.42 (0.17), residues: 1042 sheet: 0.98 (0.19), residues: 675 loop : -1.47 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 403 TYR 0.027 0.001 TYR A 453 PHE 0.026 0.001 PHE C 592 TRP 0.022 0.001 TRP D 48 HIS 0.006 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00358 (31572) covalent geometry : angle 0.62484 (42958) SS BOND : bond 0.00388 ( 45) SS BOND : angle 1.69822 ( 90) hydrogen bonds : bond 0.05231 ( 1263) hydrogen bonds : angle 4.94422 ( 3605) metal coordination : bond 0.00184 ( 2) link_BETA1-4 : bond 0.00669 ( 22) link_BETA1-4 : angle 1.83547 ( 66) link_NAG-ASN : bond 0.00372 ( 45) link_NAG-ASN : angle 2.66270 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 625 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8337 (mptt) cc_final: 0.8006 (mptt) REVERT: A 129 LYS cc_start: 0.8495 (pttp) cc_final: 0.8154 (tmmt) REVERT: A 356 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8112 (ttpp) REVERT: A 364 ASP cc_start: 0.7859 (p0) cc_final: 0.7524 (p0) REVERT: A 386 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8133 (tptp) REVERT: A 392 PHE cc_start: 0.8862 (m-80) cc_final: 0.8601 (m-80) REVERT: A 405 ASP cc_start: 0.7748 (t0) cc_final: 0.7332 (t0) REVERT: A 516 GLU cc_start: 0.6489 (tp30) cc_final: 0.5960 (tp30) REVERT: A 754 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 1031 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 52 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: B 121 ASN cc_start: 0.7016 (t0) cc_final: 0.6665 (t0) REVERT: B 304 LYS cc_start: 0.8508 (tppt) cc_final: 0.8293 (mptt) REVERT: B 532 ASN cc_start: 0.7919 (t0) cc_final: 0.7653 (t0) REVERT: B 576 VAL cc_start: 0.7481 (t) cc_final: 0.7188 (p) REVERT: B 660 TYR cc_start: 0.8784 (m-10) cc_final: 0.8580 (m-80) REVERT: B 787 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: B 814 LYS cc_start: 0.8155 (ptpp) cc_final: 0.7863 (ptpp) REVERT: B 935 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7969 (tp40) REVERT: B 1072 GLU cc_start: 0.8204 (pm20) cc_final: 0.7988 (pm20) REVERT: B 1084 ASP cc_start: 0.7369 (t70) cc_final: 0.6904 (t0) REVERT: C 343 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7506 (p0) REVERT: C 351 TYR cc_start: 0.8135 (p90) cc_final: 0.7765 (p90) REVERT: C 465 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6860 (tm-30) REVERT: C 468 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8581 (mp) REVERT: C 493 ARG cc_start: 0.6945 (mmt-90) cc_final: 0.6700 (mmt-90) REVERT: C 558 LYS cc_start: 0.8632 (mppt) cc_final: 0.8372 (mppt) REVERT: C 635 VAL cc_start: 0.5666 (OUTLIER) cc_final: 0.5395 (m) REVERT: C 646 ARG cc_start: 0.7970 (ttt-90) cc_final: 0.7680 (ttt-90) REVERT: C 776 LYS cc_start: 0.8670 (tttm) cc_final: 0.8433 (ttpp) REVERT: C 820 ASP cc_start: 0.7931 (m-30) cc_final: 0.7642 (m-30) REVERT: C 1045 LYS cc_start: 0.8265 (tppt) cc_final: 0.7900 (tppt) REVERT: C 1084 ASP cc_start: 0.7851 (t0) cc_final: 0.7389 (t0) REVERT: D 34 HIS cc_start: 0.7290 (t-90) cc_final: 0.6967 (t-90) REVERT: D 41 TYR cc_start: 0.7204 (t80) cc_final: 0.6857 (t80) REVERT: D 42 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7128 (mp10) REVERT: D 54 ILE cc_start: 0.7195 (pp) cc_final: 0.6818 (mp) REVERT: D 57 GLU cc_start: 0.7173 (pm20) cc_final: 0.6793 (pm20) REVERT: D 68 LYS cc_start: 0.8261 (mttp) cc_final: 0.8013 (mmtm) REVERT: D 97 LEU cc_start: 0.6982 (mt) cc_final: 0.6648 (tp) REVERT: D 199 TYR cc_start: 0.4560 (t80) cc_final: 0.3210 (t80) REVERT: D 203 TRP cc_start: 0.3715 (m-10) cc_final: 0.0516 (m-90) REVERT: D 309 LYS cc_start: 0.7646 (mmtt) cc_final: 0.6936 (mmtm) REVERT: D 330 ASN cc_start: 0.7365 (OUTLIER) cc_final: 0.6993 (t0) REVERT: D 375 GLU cc_start: 0.5612 (OUTLIER) cc_final: 0.5405 (pm20) REVERT: D 435 GLU cc_start: 0.4982 (tp30) cc_final: 0.4332 (tt0) REVERT: D 579 MET cc_start: 0.1226 (tpt) cc_final: -0.1009 (ttp) outliers start: 89 outliers final: 47 residues processed: 669 average time/residue: 0.6005 time to fit residues: 481.0584 Evaluate side-chains 671 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 613 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 510 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 39 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 325 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 365 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 755 GLN A1005 GLN B 196 ASN B1010 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 603 ASN C1010 GLN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN D 330 ASN D 373 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.181282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133495 restraints weight = 59668.296| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.40 r_work: 0.3515 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31686 Z= 0.210 Angle : 0.676 9.550 43249 Z= 0.338 Chirality : 0.048 0.333 4999 Planarity : 0.005 0.072 5461 Dihedral : 6.652 59.703 5472 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 2.98 % Allowed : 14.91 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 3736 helix: 1.39 (0.16), residues: 1047 sheet: 0.97 (0.19), residues: 663 loop : -1.50 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 102 TYR 0.030 0.002 TYR B 265 PHE 0.027 0.002 PHE C 592 TRP 0.019 0.001 TRP D 48 HIS 0.006 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00506 (31572) covalent geometry : angle 0.65089 (42958) SS BOND : bond 0.00433 ( 45) SS BOND : angle 1.94184 ( 90) hydrogen bonds : bond 0.05659 ( 1263) hydrogen bonds : angle 4.96552 ( 3605) metal coordination : bond 0.00294 ( 2) link_BETA1-4 : bond 0.00693 ( 22) link_BETA1-4 : angle 1.86117 ( 66) link_NAG-ASN : bond 0.00370 ( 45) link_NAG-ASN : angle 2.69522 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 633 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8347 (mptt) cc_final: 0.7989 (mptt) REVERT: A 356 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8203 (ttpp) REVERT: A 364 ASP cc_start: 0.7944 (p0) cc_final: 0.7607 (p0) REVERT: A 386 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8202 (tptp) REVERT: A 392 PHE cc_start: 0.8925 (m-80) cc_final: 0.8680 (m-80) REVERT: A 405 ASP cc_start: 0.7875 (t0) cc_final: 0.7477 (t0) REVERT: A 516 GLU cc_start: 0.6597 (tp30) cc_final: 0.6053 (tp30) REVERT: A 754 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8245 (mp) REVERT: A 1031 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7893 (mt-10) REVERT: B 52 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: B 121 ASN cc_start: 0.7077 (t0) cc_final: 0.6726 (t0) REVERT: B 304 LYS cc_start: 0.8570 (tppt) cc_final: 0.8356 (mptt) REVERT: B 532 ASN cc_start: 0.8015 (t0) cc_final: 0.7770 (t0) REVERT: B 558 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7778 (mmtp) REVERT: B 576 VAL cc_start: 0.7504 (t) cc_final: 0.7194 (p) REVERT: B 780 GLU cc_start: 0.7671 (pp20) cc_final: 0.7441 (pp20) REVERT: B 787 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: B 814 LYS cc_start: 0.8169 (ptpp) cc_final: 0.7876 (ptpp) REVERT: B 1072 GLU cc_start: 0.8277 (pm20) cc_final: 0.7973 (mp0) REVERT: B 1084 ASP cc_start: 0.7472 (t70) cc_final: 0.7009 (t0) REVERT: C 340 GLU cc_start: 0.7464 (mp0) cc_final: 0.6913 (mp0) REVERT: C 343 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7662 (p0) REVERT: C 351 TYR cc_start: 0.8218 (p90) cc_final: 0.7789 (p90) REVERT: C 465 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6935 (tm-30) REVERT: C 558 LYS cc_start: 0.8683 (mppt) cc_final: 0.8425 (mppt) REVERT: C 635 VAL cc_start: 0.5629 (OUTLIER) cc_final: 0.5338 (m) REVERT: C 776 LYS cc_start: 0.8704 (tttm) cc_final: 0.8471 (ttpp) REVERT: C 820 ASP cc_start: 0.8030 (m-30) cc_final: 0.7741 (m-30) REVERT: C 1045 LYS cc_start: 0.8365 (tppt) cc_final: 0.7986 (tppt) REVERT: C 1084 ASP cc_start: 0.7933 (t0) cc_final: 0.7447 (t0) REVERT: D 34 HIS cc_start: 0.7387 (t-90) cc_final: 0.7065 (t-90) REVERT: D 41 TYR cc_start: 0.7317 (t80) cc_final: 0.6944 (t80) REVERT: D 42 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: D 57 GLU cc_start: 0.7209 (pm20) cc_final: 0.6886 (pm20) REVERT: D 68 LYS cc_start: 0.8271 (mttp) cc_final: 0.7918 (mmtm) REVERT: D 199 TYR cc_start: 0.4648 (t80) cc_final: 0.3410 (t80) REVERT: D 203 TRP cc_start: 0.3693 (m-10) cc_final: 0.0543 (m-90) REVERT: D 309 LYS cc_start: 0.7645 (mmtt) cc_final: 0.6937 (mmtm) REVERT: D 323 MET cc_start: 0.4396 (OUTLIER) cc_final: 0.4156 (ppp) REVERT: D 330 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6909 (t0) REVERT: D 435 GLU cc_start: 0.4981 (tp30) cc_final: 0.4336 (tt0) REVERT: D 579 MET cc_start: 0.1178 (tpt) cc_final: -0.0956 (ttp) outliers start: 99 outliers final: 57 residues processed: 681 average time/residue: 0.5931 time to fit residues: 484.4232 Evaluate side-chains 692 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 624 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 408 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 127 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 184 optimal weight: 0.3980 chunk 132 optimal weight: 0.0970 chunk 367 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 336 optimal weight: 0.0000 chunk 50 optimal weight: 0.1980 overall best weight: 0.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 66 HIS A 603 ASN A 755 GLN A 901 GLN A1005 GLN B 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 603 ASN C1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.183989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137168 restraints weight = 54567.843| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.18 r_work: 0.3574 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31686 Z= 0.120 Angle : 0.643 9.791 43249 Z= 0.321 Chirality : 0.046 0.295 4999 Planarity : 0.005 0.066 5461 Dihedral : 6.336 58.980 5472 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.69 % Favored : 95.15 % Rotamer: Outliers : 2.37 % Allowed : 16.05 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3736 helix: 1.52 (0.17), residues: 1036 sheet: 1.09 (0.19), residues: 692 loop : -1.39 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 102 TYR 0.031 0.001 TYR A 453 PHE 0.029 0.001 PHE C 592 TRP 0.018 0.001 TRP D 328 HIS 0.030 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00260 (31572) covalent geometry : angle 0.62133 (42958) SS BOND : bond 0.00346 ( 45) SS BOND : angle 1.51228 ( 90) hydrogen bonds : bond 0.04608 ( 1263) hydrogen bonds : angle 4.82254 ( 3605) metal coordination : bond 0.00502 ( 2) link_BETA1-4 : bond 0.00730 ( 22) link_BETA1-4 : angle 1.85190 ( 66) link_NAG-ASN : bond 0.00432 ( 45) link_NAG-ASN : angle 2.49320 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 626 time to evaluate : 1.194 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: A 113 LYS cc_start: 0.8298 (mptt) cc_final: 0.7962 (mptt) REVERT: A 129 LYS cc_start: 0.8523 (tmmt) cc_final: 0.8305 (tmmm) REVERT: A 235 ILE cc_start: 0.8276 (mt) cc_final: 0.8053 (mm) REVERT: A 356 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8095 (ttpp) REVERT: A 364 ASP cc_start: 0.7869 (p0) cc_final: 0.7590 (p0) REVERT: A 378 LYS cc_start: 0.7803 (tmmm) cc_final: 0.7597 (tmmt) REVERT: A 386 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8098 (tptp) REVERT: A 392 PHE cc_start: 0.8872 (m-80) cc_final: 0.8611 (m-80) REVERT: A 405 ASP cc_start: 0.7693 (t0) cc_final: 0.7279 (t0) REVERT: A 406 GLU cc_start: 0.7760 (pt0) cc_final: 0.7512 (pt0) REVERT: A 516 GLU cc_start: 0.6560 (tp30) cc_final: 0.6012 (tp30) REVERT: A 754 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8207 (mp) REVERT: B 52 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: B 121 ASN cc_start: 0.6998 (t0) cc_final: 0.6594 (t0) REVERT: B 266 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.8102 (m-80) REVERT: B 304 LYS cc_start: 0.8531 (tppt) cc_final: 0.8320 (mptt) REVERT: B 532 ASN cc_start: 0.7992 (t0) cc_final: 0.7734 (t0) REVERT: B 576 VAL cc_start: 0.7440 (t) cc_final: 0.7165 (p) REVERT: B 737 ASP cc_start: 0.7615 (t0) cc_final: 0.7399 (t0) REVERT: B 780 GLU cc_start: 0.7592 (pp20) cc_final: 0.7378 (pp20) REVERT: B 787 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7588 (mp10) REVERT: B 790 LYS cc_start: 0.8276 (mppt) cc_final: 0.7922 (mtmm) REVERT: B 814 LYS cc_start: 0.8178 (ptpp) cc_final: 0.7882 (ptpp) REVERT: B 1072 GLU cc_start: 0.8260 (pm20) cc_final: 0.8022 (pm20) REVERT: B 1084 ASP cc_start: 0.7403 (t70) cc_final: 0.6938 (t0) REVERT: C 340 GLU cc_start: 0.7397 (mp0) cc_final: 0.6869 (mp0) REVERT: C 351 TYR cc_start: 0.8144 (p90) cc_final: 0.7732 (p90) REVERT: C 403 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7643 (mtp85) REVERT: C 465 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6847 (tm-30) REVERT: C 524 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8183 (p) REVERT: C 558 LYS cc_start: 0.8636 (mppt) cc_final: 0.8339 (mppt) REVERT: C 635 VAL cc_start: 0.5500 (OUTLIER) cc_final: 0.5244 (m) REVERT: C 776 LYS cc_start: 0.8654 (tttm) cc_final: 0.8424 (ttpp) REVERT: C 820 ASP cc_start: 0.7873 (m-30) cc_final: 0.7571 (m-30) REVERT: C 1045 LYS cc_start: 0.8284 (tppt) cc_final: 0.7914 (tppt) REVERT: C 1084 ASP cc_start: 0.7906 (t0) cc_final: 0.7439 (t0) REVERT: D 34 HIS cc_start: 0.7235 (t-90) cc_final: 0.6929 (t-90) REVERT: D 41 TYR cc_start: 0.7253 (t80) cc_final: 0.6882 (t80) REVERT: D 42 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: D 54 ILE cc_start: 0.6979 (pp) cc_final: 0.6526 (mm) REVERT: D 57 GLU cc_start: 0.7069 (pm20) cc_final: 0.6853 (pm20) REVERT: D 68 LYS cc_start: 0.8206 (mttp) cc_final: 0.7941 (mmtm) REVERT: D 199 TYR cc_start: 0.4609 (t80) cc_final: 0.3203 (t80) REVERT: D 203 TRP cc_start: 0.3649 (m-10) cc_final: 0.0344 (m-90) REVERT: D 309 LYS cc_start: 0.7593 (mmtt) cc_final: 0.7005 (mmtm) REVERT: D 373 HIS cc_start: 0.5681 (OUTLIER) cc_final: 0.5349 (t-90) REVERT: D 375 GLU cc_start: 0.5597 (pm20) cc_final: 0.5369 (pm20) REVERT: D 435 GLU cc_start: 0.4881 (tp30) cc_final: 0.4307 (tt0) REVERT: D 513 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6735 (tt) REVERT: D 579 MET cc_start: 0.1251 (tpt) cc_final: -0.0871 (ttp) outliers start: 79 outliers final: 44 residues processed: 670 average time/residue: 0.6008 time to fit residues: 482.5331 Evaluate side-chains 658 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 603 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 513 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 250 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 355 optimal weight: 0.0050 chunk 76 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 358 optimal weight: 0.9980 chunk 209 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 271 GLN A 603 ASN A 755 GLN A 901 GLN A1005 GLN B 196 ASN B 804 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 603 ASN C 703 ASN C1010 GLN C1135 ASN D 103 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.184003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137134 restraints weight = 51162.019| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.08 r_work: 0.3571 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31686 Z= 0.132 Angle : 0.647 11.164 43249 Z= 0.322 Chirality : 0.046 0.293 4999 Planarity : 0.005 0.096 5461 Dihedral : 6.209 58.244 5472 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.19 % Favored : 94.65 % Rotamer: Outliers : 2.10 % Allowed : 16.74 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3736 helix: 1.56 (0.17), residues: 1041 sheet: 1.18 (0.19), residues: 682 loop : -1.39 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 306 TYR 0.023 0.001 TYR A 170 PHE 0.030 0.001 PHE A 429 TRP 0.061 0.001 TRP D 328 HIS 0.007 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00302 (31572) covalent geometry : angle 0.62548 (42958) SS BOND : bond 0.00366 ( 45) SS BOND : angle 1.61838 ( 90) hydrogen bonds : bond 0.04696 ( 1263) hydrogen bonds : angle 4.77947 ( 3605) metal coordination : bond 0.00205 ( 2) link_BETA1-4 : bond 0.00665 ( 22) link_BETA1-4 : angle 1.83381 ( 66) link_NAG-ASN : bond 0.00376 ( 45) link_NAG-ASN : angle 2.45777 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 619 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8286 (mptt) cc_final: 0.7942 (mptt) REVERT: A 129 LYS cc_start: 0.8520 (tmmt) cc_final: 0.8282 (tmmm) REVERT: A 356 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8123 (ttpp) REVERT: A 378 LYS cc_start: 0.7841 (tmmm) cc_final: 0.7613 (tmmt) REVERT: A 386 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8144 (tptp) REVERT: A 392 PHE cc_start: 0.8857 (m-80) cc_final: 0.8620 (m-80) REVERT: A 405 ASP cc_start: 0.7724 (t0) cc_final: 0.7285 (t0) REVERT: A 406 GLU cc_start: 0.7820 (pt0) cc_final: 0.7583 (pt0) REVERT: A 516 GLU cc_start: 0.6607 (tp30) cc_final: 0.6092 (tp30) REVERT: A 754 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8210 (mp) REVERT: B 52 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: B 121 ASN cc_start: 0.6954 (t0) cc_final: 0.6628 (t0) REVERT: B 266 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: B 304 LYS cc_start: 0.8549 (tppt) cc_final: 0.8337 (mptt) REVERT: B 532 ASN cc_start: 0.7979 (t0) cc_final: 0.7723 (t0) REVERT: B 576 VAL cc_start: 0.7430 (t) cc_final: 0.7148 (p) REVERT: B 737 ASP cc_start: 0.7693 (t0) cc_final: 0.7422 (t0) REVERT: B 755 GLN cc_start: 0.7470 (mp10) cc_final: 0.7147 (mp10) REVERT: B 787 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: B 855 PHE cc_start: 0.8373 (m-80) cc_final: 0.8001 (m-80) REVERT: B 1072 GLU cc_start: 0.8274 (pm20) cc_final: 0.7977 (mp0) REVERT: B 1084 ASP cc_start: 0.7423 (t70) cc_final: 0.6939 (t0) REVERT: C 340 GLU cc_start: 0.7376 (mp0) cc_final: 0.6843 (mp0) REVERT: C 351 TYR cc_start: 0.8179 (p90) cc_final: 0.7768 (p90) REVERT: C 403 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7619 (ttt-90) REVERT: C 465 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6835 (tm-30) REVERT: C 524 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8224 (p) REVERT: C 558 LYS cc_start: 0.8648 (mppt) cc_final: 0.8347 (mppt) REVERT: C 635 VAL cc_start: 0.5441 (OUTLIER) cc_final: 0.5177 (m) REVERT: C 776 LYS cc_start: 0.8700 (tttm) cc_final: 0.8445 (ttpp) REVERT: C 820 ASP cc_start: 0.7887 (m-30) cc_final: 0.7559 (m-30) REVERT: C 1045 LYS cc_start: 0.8347 (tppt) cc_final: 0.7977 (tppt) REVERT: C 1084 ASP cc_start: 0.7931 (t0) cc_final: 0.7444 (t0) REVERT: D 34 HIS cc_start: 0.7294 (t-90) cc_final: 0.6967 (t-90) REVERT: D 41 TYR cc_start: 0.7290 (t80) cc_final: 0.6938 (t80) REVERT: D 42 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: D 54 ILE cc_start: 0.6913 (pp) cc_final: 0.6350 (mm) REVERT: D 57 GLU cc_start: 0.7150 (pm20) cc_final: 0.6928 (pm20) REVERT: D 68 LYS cc_start: 0.8222 (mttp) cc_final: 0.7904 (mmtm) REVERT: D 199 TYR cc_start: 0.4599 (t80) cc_final: 0.3833 (t80) REVERT: D 375 GLU cc_start: 0.5640 (OUTLIER) cc_final: 0.5374 (pm20) REVERT: D 435 GLU cc_start: 0.4883 (tp30) cc_final: 0.4316 (tt0) REVERT: D 513 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6730 (tt) REVERT: D 579 MET cc_start: 0.1178 (tpt) cc_final: -0.0947 (ttp) outliers start: 70 outliers final: 46 residues processed: 661 average time/residue: 0.6047 time to fit residues: 478.8988 Evaluate side-chains 670 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 613 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 513 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 61 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 320 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 362 optimal weight: 8.9990 chunk 210 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 271 GLN A 321 GLN A 580 GLN A 603 ASN A 755 GLN A1005 GLN B 87 ASN B 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 603 ASN C 703 ASN C1010 GLN C1135 ASN D 103 ASN D 330 ASN D 373 HIS D 380 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.181778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133409 restraints weight = 61654.630| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.54 r_work: 0.3508 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 31686 Z= 0.236 Angle : 0.716 11.024 43249 Z= 0.358 Chirality : 0.049 0.326 4999 Planarity : 0.005 0.077 5461 Dihedral : 6.307 59.507 5472 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.86 % Favored : 93.95 % Rotamer: Outliers : 2.22 % Allowed : 17.01 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3736 helix: 1.45 (0.17), residues: 1045 sheet: 1.06 (0.19), residues: 643 loop : -1.46 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 102 TYR 0.052 0.002 TYR D 454 PHE 0.037 0.002 PHE C 592 TRP 0.060 0.002 TRP D 328 HIS 0.005 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00569 (31572) covalent geometry : angle 0.69324 (42958) SS BOND : bond 0.00472 ( 45) SS BOND : angle 2.08423 ( 90) hydrogen bonds : bond 0.05843 ( 1263) hydrogen bonds : angle 4.93675 ( 3605) metal coordination : bond 0.00339 ( 2) link_BETA1-4 : bond 0.00674 ( 22) link_BETA1-4 : angle 1.85069 ( 66) link_NAG-ASN : bond 0.00405 ( 45) link_NAG-ASN : angle 2.60181 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 630 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8364 (mptt) cc_final: 0.8010 (mptt) REVERT: A 129 LYS cc_start: 0.8606 (tmmt) cc_final: 0.8394 (tmmm) REVERT: A 235 ILE cc_start: 0.8112 (mm) cc_final: 0.7902 (tp) REVERT: A 356 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8230 (ttpp) REVERT: A 378 LYS cc_start: 0.8058 (tmmm) cc_final: 0.7795 (tmmt) REVERT: A 386 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8190 (tptp) REVERT: A 392 PHE cc_start: 0.8959 (m-80) cc_final: 0.8706 (m-80) REVERT: A 405 ASP cc_start: 0.7858 (t0) cc_final: 0.7436 (t0) REVERT: A 453 TYR cc_start: 0.6679 (m-80) cc_final: 0.6346 (m-80) REVERT: A 516 GLU cc_start: 0.6697 (tp30) cc_final: 0.6124 (tp30) REVERT: A 754 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8231 (mp) REVERT: B 52 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: B 121 ASN cc_start: 0.7072 (t0) cc_final: 0.6734 (t0) REVERT: B 304 LYS cc_start: 0.8601 (tppt) cc_final: 0.8389 (mptt) REVERT: B 532 ASN cc_start: 0.8076 (t0) cc_final: 0.7829 (t0) REVERT: B 576 VAL cc_start: 0.7501 (t) cc_final: 0.7193 (p) REVERT: B 780 GLU cc_start: 0.7661 (pp20) cc_final: 0.7444 (pp20) REVERT: B 814 LYS cc_start: 0.8045 (ptpp) cc_final: 0.7803 (ptpp) REVERT: B 1072 GLU cc_start: 0.8319 (pm20) cc_final: 0.8082 (pm20) REVERT: B 1084 ASP cc_start: 0.7499 (t70) cc_final: 0.6990 (t0) REVERT: C 206 LYS cc_start: 0.8577 (tppp) cc_final: 0.8308 (tptp) REVERT: C 340 GLU cc_start: 0.7464 (mp0) cc_final: 0.6932 (mp0) REVERT: C 351 TYR cc_start: 0.8244 (p90) cc_final: 0.7826 (p90) REVERT: C 403 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7662 (ttt-90) REVERT: C 465 GLU cc_start: 0.7440 (tm-30) cc_final: 0.6962 (tm-30) REVERT: C 493 ARG cc_start: 0.7087 (mmt-90) cc_final: 0.6739 (mmt-90) REVERT: C 558 LYS cc_start: 0.8713 (mppt) cc_final: 0.8449 (mppt) REVERT: C 635 VAL cc_start: 0.5497 (OUTLIER) cc_final: 0.5204 (m) REVERT: C 646 ARG cc_start: 0.8113 (ttt-90) cc_final: 0.7741 (ttt-90) REVERT: C 776 LYS cc_start: 0.8755 (tttm) cc_final: 0.8502 (ttpp) REVERT: C 820 ASP cc_start: 0.8055 (m-30) cc_final: 0.7739 (m-30) REVERT: C 974 SER cc_start: 0.8637 (m) cc_final: 0.8412 (p) REVERT: C 1045 LYS cc_start: 0.8419 (tppt) cc_final: 0.8065 (tppt) REVERT: C 1084 ASP cc_start: 0.7988 (t0) cc_final: 0.7497 (t0) REVERT: D 34 HIS cc_start: 0.7435 (t-90) cc_final: 0.7169 (t-90) REVERT: D 41 TYR cc_start: 0.7334 (t80) cc_final: 0.6999 (t80) REVERT: D 42 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: D 54 ILE cc_start: 0.6906 (pp) cc_final: 0.6266 (mm) REVERT: D 68 LYS cc_start: 0.8260 (mttp) cc_final: 0.8005 (mmtm) REVERT: D 199 TYR cc_start: 0.4713 (t80) cc_final: 0.3976 (t80) REVERT: D 323 MET cc_start: 0.4511 (pmt) cc_final: 0.4261 (pmm) REVERT: D 330 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.6862 (t0) REVERT: D 375 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.5433 (pm20) REVERT: D 435 GLU cc_start: 0.4898 (tp30) cc_final: 0.4339 (tt0) REVERT: D 513 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.6754 (tt) REVERT: D 579 MET cc_start: 0.1189 (tpt) cc_final: -0.0843 (ttp) outliers start: 74 outliers final: 48 residues processed: 673 average time/residue: 0.6179 time to fit residues: 495.4963 Evaluate side-chains 678 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 621 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 513 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 173 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 338 optimal weight: 4.9990 chunk 320 optimal weight: 6.9990 chunk 297 optimal weight: 0.6980 chunk 147 optimal weight: 30.0000 chunk 3 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 271 GLN A 580 GLN A 603 ASN A 755 GLN A 762 GLN A1005 GLN B 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 603 ASN C1010 GLN C1135 ASN D 103 ASN D 373 HIS ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.181410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134504 restraints weight = 53456.422| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.22 r_work: 0.3530 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.169 31686 Z= 0.271 Angle : 0.981 59.199 43249 Z= 0.567 Chirality : 0.050 0.562 4999 Planarity : 0.006 0.093 5461 Dihedral : 6.312 59.519 5472 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.92 % Rotamer: Outliers : 1.83 % Allowed : 17.55 % Favored : 80.61 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3736 helix: 1.43 (0.17), residues: 1045 sheet: 1.05 (0.19), residues: 643 loop : -1.47 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 493 TYR 0.033 0.002 TYR B 265 PHE 0.033 0.002 PHE C 643 TRP 0.060 0.002 TRP D 328 HIS 0.127 0.002 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00605 (31572) covalent geometry : angle 0.96666 (42958) SS BOND : bond 0.00443 ( 45) SS BOND : angle 2.05691 ( 90) hydrogen bonds : bond 0.05851 ( 1263) hydrogen bonds : angle 4.95190 ( 3605) metal coordination : bond 0.00359 ( 2) link_BETA1-4 : bond 0.00651 ( 22) link_BETA1-4 : angle 1.85303 ( 66) link_NAG-ASN : bond 0.00404 ( 45) link_NAG-ASN : angle 2.59974 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 618 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8360 (mptt) cc_final: 0.8003 (mptt) REVERT: A 129 LYS cc_start: 0.8577 (tmmt) cc_final: 0.8347 (tmmm) REVERT: A 235 ILE cc_start: 0.8116 (mm) cc_final: 0.7901 (tp) REVERT: A 356 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8211 (ttpp) REVERT: A 378 LYS cc_start: 0.8075 (tmmm) cc_final: 0.7786 (tmmt) REVERT: A 386 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8187 (tptp) REVERT: A 392 PHE cc_start: 0.8952 (m-80) cc_final: 0.8687 (m-80) REVERT: A 405 ASP cc_start: 0.7847 (t0) cc_final: 0.7422 (t0) REVERT: A 516 GLU cc_start: 0.6672 (tp30) cc_final: 0.6088 (tp30) REVERT: A 754 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8203 (mp) REVERT: B 52 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: B 121 ASN cc_start: 0.6999 (t0) cc_final: 0.6662 (t0) REVERT: B 304 LYS cc_start: 0.8587 (tppt) cc_final: 0.8374 (mptt) REVERT: B 532 ASN cc_start: 0.8064 (t0) cc_final: 0.7809 (t0) REVERT: B 576 VAL cc_start: 0.7470 (t) cc_final: 0.7165 (p) REVERT: B 673 SER cc_start: 0.8663 (t) cc_final: 0.8457 (p) REVERT: B 780 GLU cc_start: 0.7636 (pp20) cc_final: 0.7395 (pp20) REVERT: B 814 LYS cc_start: 0.8025 (ptpp) cc_final: 0.7780 (ptpp) REVERT: B 1072 GLU cc_start: 0.8287 (pm20) cc_final: 0.8043 (pm20) REVERT: B 1084 ASP cc_start: 0.7451 (t70) cc_final: 0.6935 (t0) REVERT: C 206 LYS cc_start: 0.8556 (tppp) cc_final: 0.8260 (tptp) REVERT: C 340 GLU cc_start: 0.7428 (mp0) cc_final: 0.6882 (mp0) REVERT: C 351 TYR cc_start: 0.8245 (p90) cc_final: 0.7818 (p90) REVERT: C 403 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7655 (ttt-90) REVERT: C 465 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6909 (tm-30) REVERT: C 493 ARG cc_start: 0.7034 (mmt-90) cc_final: 0.6659 (mmt-90) REVERT: C 558 LYS cc_start: 0.8706 (mppt) cc_final: 0.8404 (mppt) REVERT: C 635 VAL cc_start: 0.5451 (OUTLIER) cc_final: 0.5159 (m) REVERT: C 646 ARG cc_start: 0.8060 (ttt-90) cc_final: 0.7680 (ttt-90) REVERT: C 776 LYS cc_start: 0.8709 (tttm) cc_final: 0.8446 (ttpp) REVERT: C 820 ASP cc_start: 0.8015 (m-30) cc_final: 0.7687 (m-30) REVERT: C 974 SER cc_start: 0.8640 (m) cc_final: 0.8399 (p) REVERT: C 1045 LYS cc_start: 0.8388 (tppt) cc_final: 0.8021 (tppt) REVERT: C 1084 ASP cc_start: 0.7962 (t0) cc_final: 0.7459 (t0) REVERT: D 34 HIS cc_start: 0.7463 (t-90) cc_final: 0.7169 (t-90) REVERT: D 41 TYR cc_start: 0.7370 (t80) cc_final: 0.7028 (t80) REVERT: D 42 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: D 54 ILE cc_start: 0.6904 (pp) cc_final: 0.6249 (mm) REVERT: D 199 TYR cc_start: 0.4772 (t80) cc_final: 0.4024 (t80) REVERT: D 375 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.5469 (pm20) REVERT: D 406 GLU cc_start: 0.7017 (tp30) cc_final: 0.6657 (tp30) REVERT: D 513 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6761 (tt) REVERT: D 579 MET cc_start: 0.1147 (tpt) cc_final: -0.0851 (ttp) outliers start: 61 outliers final: 46 residues processed: 654 average time/residue: 0.6254 time to fit residues: 485.6759 Evaluate side-chains 676 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 622 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 513 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 262 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 277 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 223 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 303 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 271 GLN A 321 GLN A 580 GLN A 603 ASN A 755 GLN A1005 GLN B 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 603 ASN C1010 GLN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.181893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135198 restraints weight = 48427.586| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.78 r_work: 0.3560 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.561 31686 Z= 0.313 Angle : 0.987 59.199 43249 Z= 0.569 Chirality : 0.050 0.562 4999 Planarity : 0.006 0.093 5461 Dihedral : 6.312 59.519 5472 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.92 % Rotamer: Outliers : 1.62 % Allowed : 17.85 % Favored : 80.52 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3736 helix: 1.43 (0.17), residues: 1045 sheet: 1.05 (0.19), residues: 643 loop : -1.47 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 493 TYR 0.033 0.002 TYR B 265 PHE 0.033 0.002 PHE C 643 TRP 0.060 0.002 TRP D 328 HIS 0.127 0.002 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00605 (31572) covalent geometry : angle 0.96666 (42958) SS BOND : bond 0.08381 ( 45) SS BOND : angle 3.05033 ( 90) hydrogen bonds : bond 0.05851 ( 1263) hydrogen bonds : angle 4.95190 ( 3605) metal coordination : bond 0.00359 ( 2) link_BETA1-4 : bond 0.00651 ( 22) link_BETA1-4 : angle 1.85303 ( 66) link_NAG-ASN : bond 0.00404 ( 45) link_NAG-ASN : angle 2.59974 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15402.58 seconds wall clock time: 261 minutes 49.36 seconds (15709.36 seconds total)