Starting phenix.real_space_refine on Wed Jun 25 07:52:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwm_32871/06_2025/7wwm_32871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwm_32871/06_2025/7wwm_32871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwm_32871/06_2025/7wwm_32871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwm_32871/06_2025/7wwm_32871.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwm_32871/06_2025/7wwm_32871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwm_32871/06_2025/7wwm_32871.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.112 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 18778 2.51 5 N 4842 2.21 5 O 5790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.49s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29536 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7765 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 53, 'TRANS': 940} Chain breaks: 8 Chain: "B" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7759 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 53, 'TRANS': 939} Chain breaks: 8 Chain: "C" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7759 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 53, 'TRANS': 939} Chain breaks: 8 Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 819 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 95} Chain: "I" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "M" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 819 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 95} Chain: "J" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 819 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 95} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" 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: "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 Time building chain proxies: 17.15, per 1000 atoms: 0.58 Number of scatterers: 29536 At special positions: 0 Unit cell: (132.614, 195.66, 205.443, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 5790 8.00 N 4842 7.00 C 18778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.16 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.00 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.58 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.16 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.86 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.87 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.16 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=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.16 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.00 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 331 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 709 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C 343 " " NAG Z 1 " - " ASN C 709 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1074 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " " NAG f 1 " - " ASN B1074 " Time building additional restraints: 7.48 Conformation dependent library (CDL) restraints added in 3.5 seconds 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6806 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 59 sheets defined 18.6% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.539A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.691A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 407' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 4.109A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.635A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.538A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.690A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.694A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.629A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.503A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 removed outlier: 4.020A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.538A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.690A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 407' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.560A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.867A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.928A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.546A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.555A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.518A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB9, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.983A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 328 removed outlier: 3.663A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.546A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.173A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.580A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD5, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.988A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.489A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.546A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.744A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.988A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.092A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AE9, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.538A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.987A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP I 73 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.091A pdb=" N GLY I 10 " --> pdb=" O THR I 119 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AF6, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AF7, first strand: chain 'M' and resid 45 through 46 removed outlier: 3.538A pdb=" N ARG M 45 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 48 through 49 Processing sheet with id=AF9, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.987A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP J 73 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.092A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 17 through 18 Processing sheet with id=AG3, first strand: chain 'N' and resid 19 through 23 Processing sheet with id=AG4, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.538A pdb=" N ARG N 45 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 48 through 49 1004 hydrogen bonds defined for protein. 2682 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: 12.31 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5248 1.32 - 1.45: 8432 1.45 - 1.57: 16366 1.57 - 1.70: 0 1.70 - 1.83: 159 Bond restraints: 30205 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.25e+01 bond pdb=" N PHE A 318 " pdb=" CA PHE A 318 " ideal model delta sigma weight residual 1.454 1.380 0.073 1.18e-02 7.18e+03 3.87e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.067 1.59e-02 3.96e+03 1.77e+01 bond pdb=" N PRO B 527 " pdb=" CD PRO B 527 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" N PRO A 561 " pdb=" CD PRO A 561 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.68e+01 ... (remaining 30200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 39874 2.73 - 5.45: 1069 5.45 - 8.18: 127 8.18 - 10.90: 15 10.90 - 13.63: 13 Bond angle restraints: 41098 Sorted by residual: angle pdb=" N PHE A 318 " pdb=" CA PHE A 318 " pdb=" C PHE A 318 " ideal model delta sigma weight residual 110.14 99.61 10.53 1.55e+00 4.16e-01 4.62e+01 angle pdb=" N PHE A 565 " pdb=" CA PHE A 565 " pdb=" C PHE A 565 " ideal model delta sigma weight residual 108.45 116.95 -8.50 1.26e+00 6.30e-01 4.55e+01 angle pdb=" N LEU C 390 " pdb=" CA LEU C 390 " pdb=" C LEU C 390 " ideal model delta sigma weight residual 108.96 118.70 -9.74 1.59e+00 3.96e-01 3.75e+01 angle pdb=" N LEU B 390 " pdb=" CA LEU B 390 " pdb=" C LEU B 390 " ideal model delta sigma weight residual 108.96 118.70 -9.74 1.59e+00 3.96e-01 3.75e+01 angle pdb=" N LEU A 390 " pdb=" CA LEU A 390 " pdb=" C LEU A 390 " ideal model delta sigma weight residual 108.96 118.66 -9.70 1.59e+00 3.96e-01 3.72e+01 ... (remaining 41093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16247 17.94 - 35.89: 1837 35.89 - 53.83: 590 53.83 - 71.77: 166 71.77 - 89.72: 43 Dihedral angle restraints: 18883 sinusoidal: 8278 harmonic: 10605 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.13 71.87 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 18880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 4814 0.329 - 0.657: 9 0.657 - 0.986: 4 0.986 - 1.315: 0 1.315 - 1.644: 2 Chirality restraints: 4829 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-02 2.50e+03 1.66e+03 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.75e+01 ... (remaining 4826 not shown) Planarity restraints: 5271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.121 2.00e-02 2.50e+03 2.15e-01 5.76e+02 pdb=" CG ASN C 331 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.381 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.145 2.00e-02 2.50e+03 1.92e-01 4.61e+02 pdb=" CG ASN A 331 " 0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.329 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.226 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.078 2.00e-02 2.50e+03 7.09e-02 6.29e+01 pdb=" CG ASN B 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.089 2.00e-02 2.50e+03 ... (remaining 5268 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 333 2.52 - 3.11: 21546 3.11 - 3.71: 42806 3.71 - 4.30: 63062 4.30 - 4.90: 105029 Nonbonded interactions: 232776 Sorted by model distance: nonbonded pdb=" O LYS B 529 " pdb=" OG SER B 530 " model vdw 1.923 3.040 nonbonded pdb=" NE2 GLN A 564 " pdb=" CD2 PHE A 565 " model vdw 1.928 3.420 nonbonded pdb=" O ASP N 50 " pdb=" OG1 THR N 51 " model vdw 1.934 3.040 nonbonded pdb=" O ASP L 50 " pdb=" OG1 THR L 51 " model vdw 1.934 3.040 nonbonded pdb=" O ASP M 50 " pdb=" OG1 THR M 51 " model vdw 1.935 3.040 ... (remaining 232771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1146 or resid 1401 thr \ ough 1408)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 1.240 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 66.080 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.200 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 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 : 0.011 0.455 30321 Z= 0.536 Angle : 1.342 49.007 41401 Z= 0.704 Chirality : 0.079 1.644 4829 Planarity : 0.009 0.122 5223 Dihedral : 17.313 89.717 11942 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 2.26 % Allowed : 12.20 % Favored : 85.54 % Rotamer: Outliers : 10.28 % Allowed : 15.91 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.11), residues: 3589 helix: -2.26 (0.16), residues: 659 sheet: -1.81 (0.16), residues: 967 loop : -3.68 (0.10), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 104 HIS 0.009 0.002 HIS A1048 PHE 0.041 0.003 PHE J 53 TYR 0.027 0.003 TYR B1067 ARG 0.007 0.001 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.05756 ( 48) link_NAG-ASN : angle 7.75997 ( 144) link_BETA1-4 : bond 0.04655 ( 23) link_BETA1-4 : angle 7.53099 ( 69) hydrogen bonds : bond 0.18032 ( 968) hydrogen bonds : angle 7.70727 ( 2682) SS BOND : bond 0.08684 ( 45) SS BOND : angle 11.95022 ( 90) covalent geometry : bond 0.01062 (30205) covalent geometry : angle 1.09311 (41098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 327 poor density : 326 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8088 (m) REVERT: A 329 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.5331 (m-10) REVERT: A 690 GLN cc_start: 0.4609 (OUTLIER) cc_final: 0.4072 (pm20) REVERT: B 66 HIS cc_start: 0.2989 (OUTLIER) cc_final: 0.2098 (m90) REVERT: C 63 THR cc_start: 0.8277 (m) cc_final: 0.8061 (m) REVERT: C 559 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.5412 (t80) REVERT: H 34 MET cc_start: 0.4046 (mmm) cc_final: 0.3464 (tmt) REVERT: H 83 MET cc_start: 0.1265 (mtm) cc_final: 0.0681 (ttm) outliers start: 327 outliers final: 85 residues processed: 610 average time/residue: 1.2432 time to fit residues: 935.1635 Evaluate side-chains 261 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 171 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 78 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 8.9990 chunk 275 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 146 optimal weight: 0.1980 chunk 284 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 329 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 188 ASN A 317 ASN A 450 ASN A 563 GLN A 644 GLN A 762 GLN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 954 GLN A 955 ASN A 969 ASN A 992 GLN A1002 GLN A1058 HIS A1101 HIS B 134 GLN B 137 ASN B 188 ASN B 317 ASN B 532 ASN B 540 ASN B 644 GLN B 655 HIS B 755 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1054 GLN C 134 GLN C 137 ASN C 239 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN M 27 GLN M 37 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.231339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143170 restraints weight = 42070.204| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 5.19 r_work: 0.3190 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30321 Z= 0.145 Angle : 0.784 14.225 41401 Z= 0.388 Chirality : 0.050 0.460 4829 Planarity : 0.006 0.068 5223 Dihedral : 9.857 64.512 5565 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.91 % Favored : 91.78 % Rotamer: Outliers : 5.72 % Allowed : 19.49 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.13), residues: 3589 helix: -0.32 (0.20), residues: 663 sheet: -1.22 (0.16), residues: 993 loop : -3.06 (0.11), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS A 519 PHE 0.028 0.002 PHE J 53 TYR 0.018 0.001 TYR A1067 ARG 0.008 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 48) link_NAG-ASN : angle 3.31977 ( 144) link_BETA1-4 : bond 0.00709 ( 23) link_BETA1-4 : angle 2.38561 ( 69) hydrogen bonds : bond 0.04811 ( 968) hydrogen bonds : angle 5.90446 ( 2682) SS BOND : bond 0.00456 ( 45) SS BOND : angle 2.32650 ( 90) covalent geometry : bond 0.00315 (30205) covalent geometry : angle 0.74825 (41098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 197 time to evaluate : 3.052 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 116 SER cc_start: 0.5798 (OUTLIER) cc_final: 0.5209 (m) REVERT: A 281 GLU cc_start: 0.7724 (pt0) cc_final: 0.7384 (pm20) REVERT: A 461 LEU cc_start: 0.0161 (OUTLIER) cc_final: -0.0347 (mt) REVERT: A 690 GLN cc_start: 0.5488 (OUTLIER) cc_final: 0.5212 (pm20) REVERT: A 794 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7756 (tp) REVERT: A 921 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7900 (mtmm) REVERT: A 988 GLU cc_start: 0.7615 (mp0) cc_final: 0.6928 (mp0) REVERT: B 66 HIS cc_start: 0.3876 (OUTLIER) cc_final: 0.2622 (m90) REVERT: B 205 SER cc_start: 0.8134 (m) cc_final: 0.7754 (p) REVERT: B 239 GLN cc_start: 0.5815 (mt0) cc_final: 0.5006 (mm-40) REVERT: B 280 ASN cc_start: 0.7752 (t0) cc_final: 0.7204 (t0) REVERT: B 529 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7478 (mptp) REVERT: B 569 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7438 (tp) REVERT: B 762 GLN cc_start: 0.8223 (mt0) cc_final: 0.7943 (mt0) REVERT: B 787 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8238 (mt0) REVERT: B 1092 GLU cc_start: 0.7795 (mp0) cc_final: 0.7592 (mt-10) REVERT: C 63 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7818 (m) REVERT: C 528 LYS cc_start: 0.5146 (OUTLIER) cc_final: 0.4154 (mptt) REVERT: C 560 LEU cc_start: 0.8164 (mp) cc_final: 0.7786 (mp) REVERT: C 564 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7257 (tp-100) REVERT: C 776 LYS cc_start: 0.8666 (tttm) cc_final: 0.8400 (ttpp) REVERT: I 70 ILE cc_start: 0.1252 (OUTLIER) cc_final: 0.0923 (tp) REVERT: M 78 LEU cc_start: 0.2392 (OUTLIER) cc_final: 0.1705 (tt) outliers start: 182 outliers final: 77 residues processed: 352 average time/residue: 1.0357 time to fit residues: 457.0423 Evaluate side-chains 240 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 149 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 78 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 155 optimal weight: 4.9990 chunk 345 optimal weight: 7.9990 chunk 349 optimal weight: 50.0000 chunk 18 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 209 optimal weight: 7.9990 chunk 325 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 271 optimal weight: 0.8980 chunk 228 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 954 GLN A1002 GLN B 81 ASN B 394 ASN B 474 GLN C 49 HIS C 239 GLN C 271 GLN C 804 GLN M 27 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.219597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.134919 restraints weight = 42172.173| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 4.38 r_work: 0.3154 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 30321 Z= 0.171 Angle : 0.749 15.097 41401 Z= 0.366 Chirality : 0.051 0.426 4829 Planarity : 0.005 0.052 5223 Dihedral : 8.644 59.756 5479 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.44 % Favored : 91.33 % Rotamer: Outliers : 5.06 % Allowed : 20.69 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.13), residues: 3589 helix: 0.24 (0.21), residues: 672 sheet: -0.93 (0.16), residues: 972 loop : -2.74 (0.12), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.005 0.001 HIS B1058 PHE 0.026 0.002 PHE J 53 TYR 0.022 0.001 TYR C1067 ARG 0.015 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 48) link_NAG-ASN : angle 3.13143 ( 144) link_BETA1-4 : bond 0.00589 ( 23) link_BETA1-4 : angle 2.26774 ( 69) hydrogen bonds : bond 0.04781 ( 968) hydrogen bonds : angle 5.59581 ( 2682) SS BOND : bond 0.00520 ( 45) SS BOND : angle 1.88129 ( 90) covalent geometry : bond 0.00402 (30205) covalent geometry : angle 0.71760 (41098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 170 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7841 (t) cc_final: 0.7610 (p) REVERT: A 116 SER cc_start: 0.5760 (OUTLIER) cc_final: 0.5367 (m) REVERT: A 226 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6152 (mp) REVERT: A 281 GLU cc_start: 0.8053 (pt0) cc_final: 0.7705 (pm20) REVERT: A 331 ASN cc_start: 0.5340 (OUTLIER) cc_final: 0.4710 (m-40) REVERT: A 461 LEU cc_start: -0.0074 (OUTLIER) cc_final: -0.0567 (mt) REVERT: A 690 GLN cc_start: 0.5508 (OUTLIER) cc_final: 0.5077 (mp10) REVERT: A 794 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7700 (tp) REVERT: A 957 GLN cc_start: 0.8391 (tp-100) cc_final: 0.7991 (tt0) REVERT: A 988 GLU cc_start: 0.7933 (mp0) cc_final: 0.7280 (mp0) REVERT: B 33 THR cc_start: 0.8630 (p) cc_final: 0.8339 (t) REVERT: B 205 SER cc_start: 0.8413 (m) cc_final: 0.7996 (p) REVERT: B 280 ASN cc_start: 0.7917 (t0) cc_final: 0.7416 (t0) REVERT: B 323 THR cc_start: 0.7055 (p) cc_final: 0.6786 (t) REVERT: B 762 GLN cc_start: 0.8448 (mt0) cc_final: 0.8158 (mt0) REVERT: B 787 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: B 811 LYS cc_start: 0.6352 (OUTLIER) cc_final: 0.5648 (mtpm) REVERT: B 867 ASP cc_start: 0.8190 (p0) cc_final: 0.7763 (m-30) REVERT: B 1045 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8435 (tptp) REVERT: B 1092 GLU cc_start: 0.8045 (mp0) cc_final: 0.7815 (mt-10) REVERT: C 63 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8042 (m) REVERT: C 190 ARG cc_start: 0.5878 (mtt90) cc_final: 0.5662 (mtt180) REVERT: C 524 VAL cc_start: -0.4252 (OUTLIER) cc_final: -0.4489 (t) REVERT: C 529 LYS cc_start: 0.7761 (tppt) cc_final: 0.7489 (tppt) REVERT: C 560 LEU cc_start: 0.8126 (mp) cc_final: 0.7851 (mp) REVERT: C 776 LYS cc_start: 0.8760 (tttm) cc_final: 0.8445 (ttpp) REVERT: C 787 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: C 794 ILE cc_start: 0.8127 (mp) cc_final: 0.7879 (tp) REVERT: C 814 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7533 (mmtp) REVERT: C 988 GLU cc_start: 0.8062 (tp30) cc_final: 0.7858 (tp30) REVERT: H 86 LEU cc_start: -0.1803 (OUTLIER) cc_final: -0.2826 (pt) REVERT: M 67 SER cc_start: 0.4750 (m) cc_final: 0.4371 (p) REVERT: M 78 LEU cc_start: 0.2748 (OUTLIER) cc_final: 0.2104 (tt) REVERT: N 4 MET cc_start: 0.2050 (ttp) cc_final: 0.1689 (ttp) outliers start: 161 outliers final: 74 residues processed: 310 average time/residue: 1.0223 time to fit residues: 395.7353 Evaluate side-chains 232 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 143 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 221 optimal weight: 6.9990 chunk 311 optimal weight: 30.0000 chunk 241 optimal weight: 7.9990 chunk 142 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 302 optimal weight: 0.7980 chunk 254 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 109 optimal weight: 20.0000 chunk 274 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN A1002 GLN B 49 HIS B 314 GLN B1106 GLN M 27 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.220190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133149 restraints weight = 42296.651| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 5.33 r_work: 0.3138 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30321 Z= 0.132 Angle : 0.694 16.152 41401 Z= 0.335 Chirality : 0.049 0.441 4829 Planarity : 0.005 0.050 5223 Dihedral : 8.044 59.125 5470 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.11 % Favored : 92.67 % Rotamer: Outliers : 4.72 % Allowed : 21.16 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.13), residues: 3589 helix: 0.67 (0.21), residues: 671 sheet: -0.72 (0.16), residues: 996 loop : -2.51 (0.12), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS B1058 PHE 0.024 0.001 PHE C 238 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 48) link_NAG-ASN : angle 3.28329 ( 144) link_BETA1-4 : bond 0.00666 ( 23) link_BETA1-4 : angle 2.18709 ( 69) hydrogen bonds : bond 0.04024 ( 968) hydrogen bonds : angle 5.34318 ( 2682) SS BOND : bond 0.00413 ( 45) SS BOND : angle 1.58155 ( 90) covalent geometry : bond 0.00296 (30205) covalent geometry : angle 0.65846 (41098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 165 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.5703 (OUTLIER) cc_final: 0.5401 (m) REVERT: A 226 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6217 (mp) REVERT: A 233 ILE cc_start: 0.5116 (OUTLIER) cc_final: 0.4901 (pt) REVERT: A 281 GLU cc_start: 0.7946 (pt0) cc_final: 0.7640 (pm20) REVERT: A 331 ASN cc_start: 0.5536 (OUTLIER) cc_final: 0.4845 (m-40) REVERT: A 461 LEU cc_start: -0.0240 (OUTLIER) cc_final: -0.0649 (tp) REVERT: A 524 VAL cc_start: 0.0543 (OUTLIER) cc_final: 0.0325 (t) REVERT: A 583 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: A 690 GLN cc_start: 0.5474 (OUTLIER) cc_final: 0.4967 (mp-120) REVERT: A 794 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7698 (tp) REVERT: A 921 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7955 (mptt) REVERT: A 957 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7754 (tt0) REVERT: A 988 GLU cc_start: 0.7957 (mp0) cc_final: 0.7290 (mp0) REVERT: B 205 SER cc_start: 0.8212 (m) cc_final: 0.7753 (p) REVERT: B 280 ASN cc_start: 0.7796 (t0) cc_final: 0.7303 (t0) REVERT: B 323 THR cc_start: 0.7118 (p) cc_final: 0.6881 (t) REVERT: B 396 TYR cc_start: 0.5509 (m-80) cc_final: 0.5301 (m-80) REVERT: B 762 GLN cc_start: 0.8131 (mt0) cc_final: 0.7784 (mt0) REVERT: B 787 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8373 (mt0) REVERT: B 867 ASP cc_start: 0.7873 (p0) cc_final: 0.7557 (m-30) REVERT: B 1045 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8219 (tptp) REVERT: C 63 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7690 (m) REVERT: C 568 ASP cc_start: 0.7374 (t0) cc_final: 0.7160 (t0) REVERT: C 675 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6447 (mp10) REVERT: C 755 GLN cc_start: 0.8405 (mp10) cc_final: 0.7759 (mt0) REVERT: C 776 LYS cc_start: 0.8656 (tttm) cc_final: 0.8141 (tttm) REVERT: C 786 LYS cc_start: 0.8553 (mptt) cc_final: 0.7975 (pttm) REVERT: C 787 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: C 988 GLU cc_start: 0.7934 (tp30) cc_final: 0.7713 (pt0) REVERT: I 70 ILE cc_start: 0.1254 (OUTLIER) cc_final: 0.0893 (tp) REVERT: M 78 LEU cc_start: 0.2486 (OUTLIER) cc_final: 0.1799 (tt) REVERT: J 98 ILE cc_start: 0.1878 (OUTLIER) cc_final: 0.1549 (mt) outliers start: 150 outliers final: 76 residues processed: 298 average time/residue: 1.0424 time to fit residues: 386.8225 Evaluate side-chains 241 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 147 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 41 optimal weight: 20.0000 chunk 324 optimal weight: 0.9990 chunk 322 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 285 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A1002 GLN B 314 GLN B 613 GLN B1106 GLN I 31 HIS I 39 GLN M 38 GLN ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.220319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.138203 restraints weight = 41861.606| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.95 r_work: 0.3102 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30321 Z= 0.195 Angle : 0.718 11.300 41401 Z= 0.348 Chirality : 0.051 0.845 4829 Planarity : 0.005 0.078 5223 Dihedral : 7.845 59.719 5466 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.16 % Favored : 91.64 % Rotamer: Outliers : 5.28 % Allowed : 20.69 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.13), residues: 3589 helix: 0.63 (0.21), residues: 671 sheet: -0.51 (0.16), residues: 1006 loop : -2.48 (0.12), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.006 0.001 HIS B1058 PHE 0.029 0.002 PHE A1075 TYR 0.024 0.001 TYR A1067 ARG 0.012 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 48) link_NAG-ASN : angle 2.78112 ( 144) link_BETA1-4 : bond 0.00669 ( 23) link_BETA1-4 : angle 2.35645 ( 69) hydrogen bonds : bond 0.04888 ( 968) hydrogen bonds : angle 5.44571 ( 2682) SS BOND : bond 0.00469 ( 45) SS BOND : angle 1.72400 ( 90) covalent geometry : bond 0.00470 (30205) covalent geometry : angle 0.68974 (41098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 151 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.5753 (OUTLIER) cc_final: 0.5497 (m) REVERT: A 233 ILE cc_start: 0.5164 (OUTLIER) cc_final: 0.4946 (pt) REVERT: A 281 GLU cc_start: 0.8252 (pt0) cc_final: 0.7849 (pm20) REVERT: A 309 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: A 331 ASN cc_start: 0.5503 (OUTLIER) cc_final: 0.4697 (m-40) REVERT: A 336 CYS cc_start: 0.0047 (OUTLIER) cc_final: -0.0505 (t) REVERT: A 461 LEU cc_start: -0.0198 (OUTLIER) cc_final: -0.0641 (tp) REVERT: A 583 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: A 794 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7831 (tp) REVERT: A 957 GLN cc_start: 0.8373 (tp-100) cc_final: 0.7996 (tt0) REVERT: A 988 GLU cc_start: 0.8202 (mp0) cc_final: 0.7443 (mp0) REVERT: B 66 HIS cc_start: 0.4030 (OUTLIER) cc_final: 0.2711 (m90) REVERT: B 205 SER cc_start: 0.8471 (m) cc_final: 0.8037 (p) REVERT: B 280 ASN cc_start: 0.7956 (t0) cc_final: 0.7503 (t0) REVERT: B 323 THR cc_start: 0.6954 (p) cc_final: 0.6670 (t) REVERT: B 565 PHE cc_start: 0.7663 (p90) cc_final: 0.7457 (p90) REVERT: B 569 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7441 (tp) REVERT: B 762 GLN cc_start: 0.8448 (mt0) cc_final: 0.8151 (mt0) REVERT: B 787 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8572 (mt0) REVERT: B 811 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6100 (mtpm) REVERT: B 867 ASP cc_start: 0.8166 (p0) cc_final: 0.7922 (m-30) REVERT: B 969 ASN cc_start: 0.9275 (OUTLIER) cc_final: 0.8834 (m110) REVERT: B 1045 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8561 (tptp) REVERT: C 63 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8106 (m) REVERT: C 568 ASP cc_start: 0.7474 (t0) cc_final: 0.7187 (t0) REVERT: C 580 GLN cc_start: 0.6803 (mm110) cc_final: 0.6564 (mm110) REVERT: C 755 GLN cc_start: 0.8518 (mp10) cc_final: 0.7938 (mt0) REVERT: C 776 LYS cc_start: 0.8863 (tttm) cc_final: 0.8566 (ttpp) REVERT: C 786 LYS cc_start: 0.8679 (mptt) cc_final: 0.8340 (pttm) REVERT: C 814 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7735 (mmtp) REVERT: C 947 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8709 (ttpt) REVERT: C 988 GLU cc_start: 0.8120 (tp30) cc_final: 0.7911 (pt0) REVERT: I 70 ILE cc_start: 0.1140 (OUTLIER) cc_final: 0.0836 (tp) REVERT: M 4 MET cc_start: 0.3075 (mmp) cc_final: 0.2768 (mtt) REVERT: M 46 LEU cc_start: 0.3655 (OUTLIER) cc_final: 0.2978 (tm) REVERT: M 78 LEU cc_start: 0.2607 (OUTLIER) cc_final: 0.1813 (tt) outliers start: 168 outliers final: 94 residues processed: 302 average time/residue: 1.0942 time to fit residues: 419.9528 Evaluate side-chains 251 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 137 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 187 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 chunk 274 optimal weight: 0.9980 chunk 250 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 341 optimal weight: 40.0000 chunk 332 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 314 GLN B 334 ASN B 703 ASN B1106 GLN I 99 HIS ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.227814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141228 restraints weight = 41540.858| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 5.09 r_work: 0.3108 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30321 Z= 0.132 Angle : 0.679 15.509 41401 Z= 0.326 Chirality : 0.052 1.328 4829 Planarity : 0.004 0.067 5223 Dihedral : 7.623 59.863 5460 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.41 % Favored : 93.42 % Rotamer: Outliers : 4.68 % Allowed : 21.57 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3589 helix: 0.97 (0.21), residues: 666 sheet: -0.37 (0.16), residues: 1005 loop : -2.33 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.002 0.001 HIS C1064 PHE 0.024 0.001 PHE I 53 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 48) link_NAG-ASN : angle 2.90458 ( 144) link_BETA1-4 : bond 0.00569 ( 23) link_BETA1-4 : angle 2.06465 ( 69) hydrogen bonds : bond 0.03997 ( 968) hydrogen bonds : angle 5.21474 ( 2682) SS BOND : bond 0.00480 ( 45) SS BOND : angle 1.55733 ( 90) covalent geometry : bond 0.00300 (30205) covalent geometry : angle 0.64976 (41098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 149 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.5656 (OUTLIER) cc_final: 0.5422 (m) REVERT: A 226 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5896 (mp) REVERT: A 233 ILE cc_start: 0.5075 (OUTLIER) cc_final: 0.4849 (pt) REVERT: A 281 GLU cc_start: 0.8171 (pt0) cc_final: 0.7824 (pm20) REVERT: A 331 ASN cc_start: 0.5580 (OUTLIER) cc_final: 0.4831 (m-40) REVERT: A 336 CYS cc_start: 0.0143 (OUTLIER) cc_final: -0.0409 (t) REVERT: A 461 LEU cc_start: -0.0215 (OUTLIER) cc_final: -0.0583 (tp) REVERT: A 583 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: A 794 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7839 (tp) REVERT: A 931 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8611 (mm) REVERT: A 957 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7771 (tt0) REVERT: A 985 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.7012 (p0) REVERT: A 988 GLU cc_start: 0.8136 (mp0) cc_final: 0.7435 (mp0) REVERT: A 1138 TYR cc_start: 0.8340 (t80) cc_final: 0.8054 (t80) REVERT: B 66 HIS cc_start: 0.4223 (OUTLIER) cc_final: 0.2881 (m90) REVERT: B 189 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6587 (mp) REVERT: B 205 SER cc_start: 0.8269 (m) cc_final: 0.7797 (p) REVERT: B 233 ILE cc_start: 0.6081 (OUTLIER) cc_final: 0.5737 (tp) REVERT: B 280 ASN cc_start: 0.7871 (t0) cc_final: 0.7422 (t0) REVERT: B 323 THR cc_start: 0.6955 (p) cc_final: 0.6741 (t) REVERT: B 524 VAL cc_start: 0.6280 (OUTLIER) cc_final: 0.5950 (p) REVERT: B 552 LEU cc_start: 0.8044 (mt) cc_final: 0.7790 (mm) REVERT: B 565 PHE cc_start: 0.7496 (p90) cc_final: 0.7251 (p90) REVERT: B 762 GLN cc_start: 0.8193 (mt0) cc_final: 0.7860 (mt0) REVERT: B 787 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8474 (mt0) REVERT: B 811 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.6182 (mtpp) REVERT: B 969 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8934 (m110) REVERT: B 1045 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8307 (tptp) REVERT: C 63 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7641 (m) REVERT: C 324 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5941 (pm20) REVERT: C 568 ASP cc_start: 0.7314 (t0) cc_final: 0.6981 (t0) REVERT: C 755 GLN cc_start: 0.8358 (mp10) cc_final: 0.7888 (mt0) REVERT: C 776 LYS cc_start: 0.8689 (tttm) cc_final: 0.8180 (tttm) REVERT: C 786 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8087 (pttm) REVERT: C 787 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.7770 (mp10) REVERT: C 796 ASP cc_start: 0.8164 (t0) cc_final: 0.7114 (p0) REVERT: C 947 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8616 (ttpt) REVERT: I 70 ILE cc_start: 0.0932 (OUTLIER) cc_final: 0.0610 (tp) REVERT: M 4 MET cc_start: 0.3219 (mmp) cc_final: 0.2888 (mtt) REVERT: M 46 LEU cc_start: 0.3698 (OUTLIER) cc_final: 0.2970 (tm) REVERT: M 78 LEU cc_start: 0.2517 (OUTLIER) cc_final: 0.1762 (tp) REVERT: J 98 ILE cc_start: 0.1965 (OUTLIER) cc_final: 0.1688 (mt) outliers start: 149 outliers final: 79 residues processed: 278 average time/residue: 0.9983 time to fit residues: 348.5032 Evaluate side-chains 243 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 137 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 17 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 352 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 236 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 935 GLN A1002 GLN B 314 GLN B 703 ASN B1106 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1106 GLN J 39 GLN J 99 HIS ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** N 90 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 = 0.4576 r_free = 0.4576 target = 0.221352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133130 restraints weight = 41025.042| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 5.09 r_work: 0.3060 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 30321 Z= 0.230 Angle : 0.740 14.410 41401 Z= 0.359 Chirality : 0.052 0.758 4829 Planarity : 0.005 0.060 5223 Dihedral : 7.594 59.633 5457 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.25 % Favored : 91.61 % Rotamer: Outliers : 4.72 % Allowed : 22.04 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.13), residues: 3589 helix: 0.70 (0.21), residues: 668 sheet: -0.41 (0.16), residues: 1004 loop : -2.29 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.006 0.001 HIS B1058 PHE 0.023 0.002 PHE I 53 TYR 0.025 0.001 TYR A1067 ARG 0.006 0.001 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 48) link_NAG-ASN : angle 2.91601 ( 144) link_BETA1-4 : bond 0.00528 ( 23) link_BETA1-4 : angle 2.18983 ( 69) hydrogen bonds : bond 0.05165 ( 968) hydrogen bonds : angle 5.46874 ( 2682) SS BOND : bond 0.00558 ( 45) SS BOND : angle 1.73365 ( 90) covalent geometry : bond 0.00563 (30205) covalent geometry : angle 0.71194 (41098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 129 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.5844 (OUTLIER) cc_final: 0.5644 (m) REVERT: A 226 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5914 (mp) REVERT: A 233 ILE cc_start: 0.5137 (OUTLIER) cc_final: 0.4922 (pt) REVERT: A 281 GLU cc_start: 0.8362 (pt0) cc_final: 0.8018 (pm20) REVERT: A 331 ASN cc_start: 0.5589 (OUTLIER) cc_final: 0.4863 (m-40) REVERT: A 336 CYS cc_start: 0.0708 (OUTLIER) cc_final: 0.0022 (t) REVERT: A 461 LEU cc_start: -0.0778 (OUTLIER) cc_final: -0.1055 (tp) REVERT: A 957 GLN cc_start: 0.8392 (tp-100) cc_final: 0.8014 (tt0) REVERT: A 988 GLU cc_start: 0.8148 (mp0) cc_final: 0.7512 (mp0) REVERT: A 1045 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8852 (mmmt) REVERT: A 1138 TYR cc_start: 0.8437 (t80) cc_final: 0.8162 (t80) REVERT: B 66 HIS cc_start: 0.4250 (OUTLIER) cc_final: 0.2892 (m90) REVERT: B 205 SER cc_start: 0.8478 (m) cc_final: 0.8033 (p) REVERT: B 233 ILE cc_start: 0.6234 (OUTLIER) cc_final: 0.5921 (tp) REVERT: B 280 ASN cc_start: 0.7960 (t0) cc_final: 0.7466 (t0) REVERT: B 319 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8256 (mtp180) REVERT: B 565 PHE cc_start: 0.7819 (p90) cc_final: 0.7594 (p90) REVERT: B 569 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7390 (tp) REVERT: B 762 GLN cc_start: 0.8478 (mt0) cc_final: 0.8175 (mt0) REVERT: B 787 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8672 (mt0) REVERT: B 811 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6059 (mtpp) REVERT: B 1045 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8588 (tptp) REVERT: C 324 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6686 (pm20) REVERT: C 568 ASP cc_start: 0.7610 (t0) cc_final: 0.7288 (t0) REVERT: C 675 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6387 (mp10) REVERT: C 755 GLN cc_start: 0.8573 (mp10) cc_final: 0.8070 (mt0) REVERT: C 776 LYS cc_start: 0.8887 (tttm) cc_final: 0.8624 (ttpp) REVERT: C 786 LYS cc_start: 0.8711 (mptt) cc_final: 0.8376 (pttm) REVERT: C 796 ASP cc_start: 0.8503 (t0) cc_final: 0.7394 (p0) REVERT: C 947 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8732 (ttpt) REVERT: I 70 ILE cc_start: 0.0955 (OUTLIER) cc_final: 0.0609 (tp) REVERT: M 4 MET cc_start: 0.3239 (mmp) cc_final: 0.2832 (mtt) REVERT: M 46 LEU cc_start: 0.3875 (OUTLIER) cc_final: 0.2988 (tm) REVERT: M 78 LEU cc_start: 0.2235 (OUTLIER) cc_final: 0.1525 (tp) REVERT: J 98 ILE cc_start: 0.1971 (OUTLIER) cc_final: 0.1682 (mt) outliers start: 150 outliers final: 87 residues processed: 264 average time/residue: 1.0276 time to fit residues: 342.2180 Evaluate side-chains 231 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 123 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 98 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 131 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 259 optimal weight: 0.0670 chunk 336 optimal weight: 0.0470 chunk 217 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 935 GLN A1002 GLN B 703 ASN B1106 GLN C 121 ASN C 580 GLN C 960 ASN ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.224577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.140279 restraints weight = 41859.611| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 5.07 r_work: 0.3112 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30321 Z= 0.117 Angle : 0.654 11.702 41401 Z= 0.315 Chirality : 0.048 0.548 4829 Planarity : 0.004 0.053 5223 Dihedral : 7.057 58.652 5453 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.16 % Favored : 93.68 % Rotamer: Outliers : 3.99 % Allowed : 22.45 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3589 helix: 1.16 (0.21), residues: 667 sheet: -0.18 (0.16), residues: 1010 loop : -2.22 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS A1058 PHE 0.024 0.001 PHE J 53 TYR 0.017 0.001 TYR C1067 ARG 0.003 0.000 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 48) link_NAG-ASN : angle 2.43093 ( 144) link_BETA1-4 : bond 0.00514 ( 23) link_BETA1-4 : angle 1.94801 ( 69) hydrogen bonds : bond 0.03788 ( 968) hydrogen bonds : angle 5.13106 ( 2682) SS BOND : bond 0.00404 ( 45) SS BOND : angle 1.46810 ( 90) covalent geometry : bond 0.00262 (30205) covalent geometry : angle 0.63224 (41098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 139 time to evaluate : 3.496 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 226 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5820 (mp) REVERT: A 233 ILE cc_start: 0.5041 (OUTLIER) cc_final: 0.4830 (pt) REVERT: A 281 GLU cc_start: 0.8257 (pt0) cc_final: 0.7972 (pm20) REVERT: A 331 ASN cc_start: 0.5720 (OUTLIER) cc_final: 0.4976 (m-40) REVERT: A 336 CYS cc_start: 0.0468 (OUTLIER) cc_final: -0.0146 (t) REVERT: A 461 LEU cc_start: -0.0163 (OUTLIER) cc_final: -0.0502 (tp) REVERT: A 554 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7086 (mm-30) REVERT: A 583 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: A 931 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8640 (mm) REVERT: A 957 GLN cc_start: 0.8151 (tp-100) cc_final: 0.7793 (tt0) REVERT: A 988 GLU cc_start: 0.8184 (mp0) cc_final: 0.7430 (mp0) REVERT: A 1045 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8764 (mmmt) REVERT: A 1138 TYR cc_start: 0.8291 (t80) cc_final: 0.8024 (t80) REVERT: B 66 HIS cc_start: 0.4249 (OUTLIER) cc_final: 0.2890 (m90) REVERT: B 205 SER cc_start: 0.8209 (m) cc_final: 0.7672 (p) REVERT: B 233 ILE cc_start: 0.6245 (OUTLIER) cc_final: 0.5917 (tp) REVERT: B 280 ASN cc_start: 0.7899 (t0) cc_final: 0.7459 (t0) REVERT: B 524 VAL cc_start: 0.6578 (OUTLIER) cc_final: 0.6262 (p) REVERT: B 552 LEU cc_start: 0.8078 (mt) cc_final: 0.7821 (mm) REVERT: B 565 PHE cc_start: 0.7480 (p90) cc_final: 0.7275 (p90) REVERT: B 762 GLN cc_start: 0.8130 (mt0) cc_final: 0.7809 (mt0) REVERT: B 787 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8532 (mt0) REVERT: B 1045 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8350 (tptp) REVERT: C 324 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6592 (pm20) REVERT: C 568 ASP cc_start: 0.7362 (t0) cc_final: 0.7023 (t0) REVERT: C 755 GLN cc_start: 0.8460 (mp10) cc_final: 0.8046 (mt0) REVERT: C 776 LYS cc_start: 0.8726 (tttm) cc_final: 0.8196 (tttm) REVERT: C 786 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8239 (pttm) REVERT: C 947 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8605 (ttpt) REVERT: I 70 ILE cc_start: 0.0809 (OUTLIER) cc_final: 0.0510 (tp) REVERT: M 46 LEU cc_start: 0.3393 (OUTLIER) cc_final: 0.2672 (tm) REVERT: M 78 LEU cc_start: 0.3122 (OUTLIER) cc_final: 0.2230 (tp) REVERT: J 98 ILE cc_start: 0.2332 (OUTLIER) cc_final: 0.2080 (mt) outliers start: 127 outliers final: 78 residues processed: 250 average time/residue: 1.0122 time to fit residues: 318.2051 Evaluate side-chains 227 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 129 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 334 optimal weight: 50.0000 chunk 106 optimal weight: 4.9990 chunk 312 optimal weight: 10.0000 chunk 284 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 chunk 246 optimal weight: 9.9990 chunk 31 optimal weight: 50.0000 chunk 142 optimal weight: 3.9990 chunk 335 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 935 GLN B 703 ASN B1106 GLN C 580 GLN C 960 ASN ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.223646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.144439 restraints weight = 43172.300| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.26 r_work: 0.3376 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 30321 Z= 0.244 Angle : 0.754 13.523 41401 Z= 0.365 Chirality : 0.052 0.537 4829 Planarity : 0.005 0.055 5223 Dihedral : 7.733 98.396 5453 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.33 % Favored : 91.53 % Rotamer: Outliers : 4.21 % Allowed : 22.67 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3589 helix: 0.83 (0.21), residues: 663 sheet: -0.24 (0.16), residues: 984 loop : -2.27 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.007 0.001 HIS B1058 PHE 0.024 0.002 PHE C 86 TYR 0.026 0.001 TYR A1067 ARG 0.007 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 48) link_NAG-ASN : angle 2.64055 ( 144) link_BETA1-4 : bond 0.00531 ( 23) link_BETA1-4 : angle 2.38836 ( 69) hydrogen bonds : bond 0.05326 ( 968) hydrogen bonds : angle 5.43152 ( 2682) SS BOND : bond 0.00536 ( 45) SS BOND : angle 1.79595 ( 90) covalent geometry : bond 0.00596 (30205) covalent geometry : angle 0.72952 (41098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 132 time to evaluate : 3.107 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 200 TYR cc_start: 0.7764 (m-80) cc_final: 0.7479 (m-80) REVERT: A 226 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5969 (mp) REVERT: A 281 GLU cc_start: 0.8417 (pt0) cc_final: 0.8130 (pm20) REVERT: A 331 ASN cc_start: 0.6011 (OUTLIER) cc_final: 0.5210 (m-40) REVERT: A 461 LEU cc_start: -0.0596 (OUTLIER) cc_final: -0.0829 (tp) REVERT: A 524 VAL cc_start: 0.0297 (OUTLIER) cc_final: 0.0092 (t) REVERT: A 554 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 690 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.5549 (mp10) REVERT: A 957 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7926 (tt0) REVERT: A 988 GLU cc_start: 0.8166 (mp0) cc_final: 0.7396 (mp0) REVERT: A 1002 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8379 (tp40) REVERT: A 1045 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8736 (mmmt) REVERT: A 1138 TYR cc_start: 0.8517 (t80) cc_final: 0.8279 (t80) REVERT: B 66 HIS cc_start: 0.4441 (OUTLIER) cc_final: 0.2926 (m90) REVERT: B 203 ILE cc_start: 0.7596 (mt) cc_final: 0.7031 (tt) REVERT: B 226 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5389 (pt) REVERT: B 233 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5976 (tp) REVERT: B 280 ASN cc_start: 0.7969 (t0) cc_final: 0.7501 (t0) REVERT: B 319 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8187 (mtp180) REVERT: B 552 LEU cc_start: 0.8289 (mt) cc_final: 0.8016 (mm) REVERT: B 565 PHE cc_start: 0.7854 (p90) cc_final: 0.7603 (p90) REVERT: B 762 GLN cc_start: 0.8418 (mt0) cc_final: 0.8115 (mt0) REVERT: B 787 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8563 (mt0) REVERT: B 1045 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8468 (tptp) REVERT: C 324 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: C 568 ASP cc_start: 0.7414 (t0) cc_final: 0.7105 (t0) REVERT: C 675 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6349 (mp10) REVERT: C 755 GLN cc_start: 0.8522 (mp10) cc_final: 0.8118 (mt0) REVERT: C 776 LYS cc_start: 0.8834 (tttm) cc_final: 0.8563 (ttpp) REVERT: C 786 LYS cc_start: 0.8671 (mptt) cc_final: 0.8337 (pttm) REVERT: C 947 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8678 (ttpt) REVERT: I 70 ILE cc_start: 0.0592 (OUTLIER) cc_final: 0.0293 (tp) REVERT: M 46 LEU cc_start: 0.4002 (OUTLIER) cc_final: 0.3114 (tm) REVERT: M 78 LEU cc_start: 0.2130 (OUTLIER) cc_final: 0.1353 (tp) outliers start: 134 outliers final: 85 residues processed: 249 average time/residue: 1.0454 time to fit residues: 333.7959 Evaluate side-chains 232 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 128 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 343 optimal weight: 7.9990 chunk 193 optimal weight: 0.8980 chunk 295 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 130 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 112 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 297 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 935 GLN A1002 GLN B 703 ASN B1106 GLN ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.227542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.148977 restraints weight = 43083.995| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 4.61 r_work: 0.3389 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30321 Z= 0.122 Angle : 0.668 11.888 41401 Z= 0.321 Chirality : 0.048 0.519 4829 Planarity : 0.004 0.056 5223 Dihedral : 7.517 112.767 5452 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.41 % Favored : 93.42 % Rotamer: Outliers : 3.43 % Allowed : 23.45 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3589 helix: 1.21 (0.21), residues: 666 sheet: -0.11 (0.17), residues: 993 loop : -2.15 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.003 0.001 HIS H 84 PHE 0.024 0.001 PHE J 53 TYR 0.017 0.001 TYR C1067 ARG 0.002 0.000 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 48) link_NAG-ASN : angle 2.32735 ( 144) link_BETA1-4 : bond 0.00588 ( 23) link_BETA1-4 : angle 2.06851 ( 69) hydrogen bonds : bond 0.03837 ( 968) hydrogen bonds : angle 5.10104 ( 2682) SS BOND : bond 0.00390 ( 45) SS BOND : angle 1.35750 ( 90) covalent geometry : bond 0.00276 (30205) covalent geometry : angle 0.64710 (41098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 131 time to evaluate : 3.164 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 226 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5910 (mp) REVERT: A 281 GLU cc_start: 0.8401 (pt0) cc_final: 0.8111 (pm20) REVERT: A 331 ASN cc_start: 0.5918 (OUTLIER) cc_final: 0.5122 (m-40) REVERT: A 931 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8659 (mm) REVERT: A 957 GLN cc_start: 0.8292 (tp-100) cc_final: 0.7926 (tt0) REVERT: A 988 GLU cc_start: 0.8200 (mp0) cc_final: 0.7473 (mp0) REVERT: A 1045 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8749 (mmmt) REVERT: A 1138 TYR cc_start: 0.8392 (t80) cc_final: 0.8134 (t80) REVERT: B 66 HIS cc_start: 0.4309 (OUTLIER) cc_final: 0.2838 (m90) REVERT: B 233 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.5998 (tp) REVERT: B 280 ASN cc_start: 0.8001 (t0) cc_final: 0.7597 (t0) REVERT: B 524 VAL cc_start: 0.6616 (OUTLIER) cc_final: 0.6289 (p) REVERT: B 552 LEU cc_start: 0.8305 (mt) cc_final: 0.8067 (mm) REVERT: B 565 PHE cc_start: 0.7678 (p90) cc_final: 0.7472 (p90) REVERT: B 675 GLN cc_start: 0.7347 (tt0) cc_final: 0.7114 (tm-30) REVERT: B 762 GLN cc_start: 0.8312 (mt0) cc_final: 0.8010 (mt0) REVERT: B 787 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8672 (mt0) REVERT: B 1045 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8404 (tptp) REVERT: C 324 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6791 (pm20) REVERT: C 546 LEU cc_start: 0.7211 (tp) cc_final: 0.6727 (pp) REVERT: C 568 ASP cc_start: 0.7451 (t0) cc_final: 0.7103 (t0) REVERT: C 755 GLN cc_start: 0.8554 (mp10) cc_final: 0.8157 (mt0) REVERT: C 776 LYS cc_start: 0.8755 (tttm) cc_final: 0.8231 (tttm) REVERT: C 786 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8403 (pttm) REVERT: I 70 ILE cc_start: 0.0681 (OUTLIER) cc_final: 0.0349 (tp) REVERT: M 46 LEU cc_start: 0.4150 (OUTLIER) cc_final: 0.3175 (tm) REVERT: M 78 LEU cc_start: 0.1989 (OUTLIER) cc_final: 0.1307 (tp) REVERT: J 98 ILE cc_start: 0.1579 (OUTLIER) cc_final: 0.1362 (pp) outliers start: 109 outliers final: 73 residues processed: 226 average time/residue: 1.0417 time to fit residues: 296.5413 Evaluate side-chains 216 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 128 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 204 optimal weight: 0.0670 chunk 173 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 301 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 333 optimal weight: 40.0000 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 935 GLN A1002 GLN B 121 ASN B 703 ASN B1106 GLN C 960 ASN ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.236001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.154136 restraints weight = 43279.777| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 4.62 r_work: 0.3426 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30321 Z= 0.111 Angle : 0.646 11.723 41401 Z= 0.310 Chirality : 0.047 0.486 4829 Planarity : 0.004 0.058 5223 Dihedral : 7.150 111.802 5449 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.66 % Favored : 93.17 % Rotamer: Outliers : 2.89 % Allowed : 24.14 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3589 helix: 1.44 (0.22), residues: 660 sheet: 0.03 (0.16), residues: 1001 loop : -2.11 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.005 0.000 HIS H 84 PHE 0.023 0.001 PHE J 53 TYR 0.018 0.001 TYR A1067 ARG 0.002 0.000 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 48) link_NAG-ASN : angle 2.20565 ( 144) link_BETA1-4 : bond 0.00574 ( 23) link_BETA1-4 : angle 1.98433 ( 69) hydrogen bonds : bond 0.03501 ( 968) hydrogen bonds : angle 4.91781 ( 2682) SS BOND : bond 0.00403 ( 45) SS BOND : angle 1.32460 ( 90) covalent geometry : bond 0.00248 (30205) covalent geometry : angle 0.62720 (41098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34082.04 seconds wall clock time: 595 minutes 40.28 seconds (35740.28 seconds total)