Starting phenix.real_space_refine on Fri Mar 6 07:50:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwm_32871/03_2026/7wwm_32871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwm_32871/03_2026/7wwm_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wwm_32871/03_2026/7wwm_32871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwm_32871/03_2026/7wwm_32871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wwm_32871/03_2026/7wwm_32871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwm_32871/03_2026/7wwm_32871.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.59, per 1000 atoms: 0.22 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: 2.48 Conformation dependent library (CDL) restraints added in 1.3 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: 1.36 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: 9.06 Time building geometry restraints manager: 3.22 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 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: 2.160 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: 0.040 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.490 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 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:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.180 ------------------------------------------------------------------------------- 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 : 22.63 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (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 ARG 0.007 0.001 ARG A1039 TYR 0.027 0.003 TYR B1067 PHE 0.041 0.003 PHE J 53 TRP 0.025 0.003 TRP C 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01062 (30205) covalent geometry : angle 1.09311 (41098) SS BOND : bond 0.08684 ( 45) SS BOND : angle 11.95022 ( 90) hydrogen bonds : bond 0.18032 ( 968) hydrogen bonds : angle 7.70727 ( 2682) link_BETA1-4 : bond 0.04655 ( 23) link_BETA1-4 : angle 7.53099 ( 69) link_NAG-ASN : bond 0.05756 ( 48) link_NAG-ASN : angle 7.75997 ( 144) *********************** 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 : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8085 (m) REVERT: A 329 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.5334 (m-10) REVERT: B 66 HIS cc_start: 0.2989 (OUTLIER) cc_final: 0.2100 (m90) REVERT: C 63 THR cc_start: 0.8277 (m) cc_final: 0.8062 (m) REVERT: H 34 MET cc_start: 0.4046 (mmm) cc_final: 0.3465 (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: 0.5152 time to fit residues: 381.3579 Evaluate side-chains 260 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 172 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 386 LYS Chi-restraints excluded: chain A residue 457 ARG 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 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 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 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 856 ASN 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 271 GLN 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 394 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 271 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: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.227417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.147184 restraints weight = 42776.716| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 4.11 r_work: 0.3165 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30321 Z= 0.160 Angle : 0.795 14.681 41401 Z= 0.393 Chirality : 0.051 0.451 4829 Planarity : 0.006 0.069 5223 Dihedral : 9.809 65.883 5560 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.14 % Favored : 91.56 % Rotamer: Outliers : 5.94 % Allowed : 19.40 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.12), residues: 3589 helix: -0.41 (0.20), residues: 667 sheet: -1.22 (0.16), residues: 985 loop : -3.08 (0.11), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 357 TYR 0.018 0.001 TYR A1067 PHE 0.028 0.002 PHE J 53 TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00358 (30205) covalent geometry : angle 0.75670 (41098) SS BOND : bond 0.00482 ( 45) SS BOND : angle 2.45195 ( 90) hydrogen bonds : bond 0.05056 ( 968) hydrogen bonds : angle 5.93424 ( 2682) link_BETA1-4 : bond 0.00740 ( 23) link_BETA1-4 : angle 2.40472 ( 69) link_NAG-ASN : bond 0.00459 ( 48) link_NAG-ASN : angle 3.43036 ( 144) *********************** 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 381 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 192 time to evaluate : 1.057 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: 0.5861 (OUTLIER) cc_final: 0.5293 (m) REVERT: A 461 LEU cc_start: 0.0347 (OUTLIER) cc_final: -0.0416 (mt) REVERT: A 563 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6337 (mp10) REVERT: A 565 PHE cc_start: 0.6352 (OUTLIER) cc_final: 0.6137 (p90) REVERT: A 787 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8793 (mt0) REVERT: A 794 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7774 (tp) REVERT: A 921 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7712 (mptt) REVERT: A 988 GLU cc_start: 0.7663 (mp0) cc_final: 0.7008 (mp0) REVERT: B 66 HIS cc_start: 0.3912 (OUTLIER) cc_final: 0.2634 (m90) REVERT: B 205 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7810 (p) REVERT: B 280 ASN cc_start: 0.7777 (t0) cc_final: 0.7204 (t0) REVERT: B 529 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7503 (mptp) REVERT: B 569 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7429 (tp) REVERT: B 762 GLN cc_start: 0.8233 (mt0) cc_final: 0.7953 (mt0) REVERT: B 787 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: B 1092 GLU cc_start: 0.7825 (mp0) cc_final: 0.7607 (mt-10) REVERT: C 28 TYR cc_start: 0.7987 (m-80) cc_final: 0.7725 (m-80) REVERT: C 63 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7860 (m) REVERT: C 271 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: C 524 VAL cc_start: -0.4446 (OUTLIER) cc_final: -0.4685 (t) REVERT: C 564 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7090 (tp-100) REVERT: C 776 LYS cc_start: 0.8672 (tttm) cc_final: 0.8389 (ttpp) REVERT: I 70 ILE cc_start: 0.1192 (OUTLIER) cc_final: 0.0870 (tp) REVERT: M 78 LEU cc_start: 0.2194 (OUTLIER) cc_final: 0.1523 (tt) outliers start: 189 outliers final: 82 residues processed: 351 average time/residue: 0.4897 time to fit residues: 212.1718 Evaluate side-chains 248 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 148 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 221 SER Chi-restraints excluded: chain A residue 298 GLU 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 386 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE 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 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 787 GLN 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 967 SER 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 205 SER 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 553 THR 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 271 GLN 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 524 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 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 591 SER Chi-restraints excluded: chain C residue 608 VAL 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 202 optimal weight: 0.0770 chunk 359 optimal weight: 30.0000 chunk 38 optimal weight: 40.0000 chunk 310 optimal weight: 40.0000 chunk 97 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 292 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 341 optimal weight: 30.0000 chunk 301 optimal weight: 5.9990 chunk 166 optimal weight: 0.3980 overall best weight: 2.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 271 GLN A 563 GLN A 954 GLN A1002 GLN B 81 ASN B 314 GLN B 474 GLN C 49 HIS C 239 GLN C 804 GLN M 27 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.222566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136284 restraints weight = 42218.911| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 4.16 r_work: 0.3137 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30321 Z= 0.177 Angle : 0.761 13.740 41401 Z= 0.371 Chirality : 0.052 0.781 4829 Planarity : 0.005 0.052 5223 Dihedral : 8.741 60.996 5479 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.55 % Favored : 91.22 % Rotamer: Outliers : 5.16 % Allowed : 20.43 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.13), residues: 3589 helix: 0.21 (0.21), residues: 672 sheet: -0.93 (0.16), residues: 977 loop : -2.76 (0.12), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 237 TYR 0.022 0.001 TYR C1067 PHE 0.026 0.002 PHE J 53 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00420 (30205) covalent geometry : angle 0.72813 (41098) SS BOND : bond 0.00534 ( 45) SS BOND : angle 1.91286 ( 90) hydrogen bonds : bond 0.04883 ( 968) hydrogen bonds : angle 5.63084 ( 2682) link_BETA1-4 : bond 0.00590 ( 23) link_BETA1-4 : angle 2.35574 ( 69) link_NAG-ASN : bond 0.00409 ( 48) link_NAG-ASN : angle 3.17315 ( 144) *********************** 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: 164 poor density : 167 time to evaluate : 0.784 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: 0.7920 (t) cc_final: 0.7710 (p) REVERT: A 116 SER cc_start: 0.5772 (OUTLIER) cc_final: 0.5359 (m) REVERT: A 226 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6181 (mp) REVERT: A 281 GLU cc_start: 0.7913 (pt0) cc_final: 0.7560 (pm20) REVERT: A 331 ASN cc_start: 0.5504 (OUTLIER) cc_final: 0.4866 (m-40) REVERT: A 461 LEU cc_start: -0.0135 (OUTLIER) cc_final: -0.0632 (mt) REVERT: A 794 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7734 (tp) REVERT: A 921 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8056 (mptt) REVERT: A 957 GLN cc_start: 0.8391 (tp-100) cc_final: 0.7990 (tt0) REVERT: A 988 GLU cc_start: 0.7920 (mp0) cc_final: 0.7219 (mp0) REVERT: B 205 SER cc_start: 0.8451 (m) cc_final: 0.8041 (p) REVERT: B 280 ASN cc_start: 0.7909 (t0) cc_final: 0.7422 (t0) REVERT: B 323 THR cc_start: 0.7024 (p) cc_final: 0.6730 (t) REVERT: B 396 TYR cc_start: 0.4335 (m-80) cc_final: 0.4097 (m-80) REVERT: B 762 GLN cc_start: 0.8434 (mt0) cc_final: 0.8176 (mt0) REVERT: B 787 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8489 (mt0) REVERT: B 811 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5754 (mptt) REVERT: B 855 PHE cc_start: 0.7532 (m-80) cc_final: 0.7261 (m-80) REVERT: B 867 ASP cc_start: 0.8199 (p0) cc_final: 0.7777 (m-30) REVERT: B 1045 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8463 (tptp) REVERT: B 1092 GLU cc_start: 0.8025 (mp0) cc_final: 0.7785 (mt-10) REVERT: C 63 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8164 (m) REVERT: C 190 ARG cc_start: 0.6360 (OUTLIER) cc_final: 0.6132 (mtt-85) REVERT: C 324 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.5754 (pm20) REVERT: C 776 LYS cc_start: 0.8781 (tttm) cc_final: 0.8522 (ttpp) REVERT: C 787 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: C 794 ILE cc_start: 0.8135 (mp) cc_final: 0.7889 (tp) REVERT: H 83 MET cc_start: -0.1687 (ttm) cc_final: -0.1904 (ttp) REVERT: H 86 LEU cc_start: -0.1808 (OUTLIER) cc_final: -0.2838 (pt) REVERT: I 70 ILE cc_start: 0.1386 (OUTLIER) cc_final: 0.1040 (tp) REVERT: M 67 SER cc_start: 0.4765 (m) cc_final: 0.4402 (p) REVERT: M 78 LEU cc_start: 0.2378 (OUTLIER) cc_final: 0.1857 (tt) REVERT: N 4 MET cc_start: 0.1850 (ttp) cc_final: 0.1532 (ttp) outliers start: 164 outliers final: 73 residues processed: 310 average time/residue: 0.4846 time to fit residues: 184.6420 Evaluate side-chains 231 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 142 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 576 VAL 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 921 LYS 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 994 ASP 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 B residue 36 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 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 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 998 THR 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 190 ARG 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 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 608 VAL 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 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 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 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 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 122 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 290 optimal weight: 4.9990 chunk 114 optimal weight: 0.2980 chunk 288 optimal weight: 0.5980 chunk 108 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 329 optimal weight: 4.9990 chunk 348 optimal weight: 30.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 B 613 GLN B1106 GLN C 188 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 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 = 0.4611 r_free = 0.4611 target = 0.222935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.140702 restraints weight = 42393.154| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 4.10 r_work: 0.3172 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3307 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= 0.134 Angle : 0.699 17.316 41401 Z= 0.337 Chirality : 0.049 0.684 4829 Planarity : 0.005 0.055 5223 Dihedral : 8.156 59.612 5466 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.16 % Favored : 92.62 % Rotamer: Outliers : 4.68 % Allowed : 20.97 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.13), residues: 3589 helix: 0.65 (0.21), residues: 668 sheet: -0.73 (0.16), residues: 973 loop : -2.49 (0.12), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.018 0.001 TYR A1067 PHE 0.024 0.001 PHE C 238 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00300 (30205) covalent geometry : angle 0.66281 (41098) SS BOND : bond 0.00508 ( 45) SS BOND : angle 1.64914 ( 90) hydrogen bonds : bond 0.04074 ( 968) hydrogen bonds : angle 5.36989 ( 2682) link_BETA1-4 : bond 0.00671 ( 23) link_BETA1-4 : angle 2.22422 ( 69) link_NAG-ASN : bond 0.00892 ( 48) link_NAG-ASN : angle 3.29047 ( 144) *********************** 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 310 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 161 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.5707 (OUTLIER) cc_final: 0.5424 (m) REVERT: A 233 ILE cc_start: 0.5056 (OUTLIER) cc_final: 0.4853 (pt) REVERT: A 281 GLU cc_start: 0.8014 (pt0) cc_final: 0.7654 (pm20) REVERT: A 331 ASN cc_start: 0.5435 (OUTLIER) cc_final: 0.4775 (m-40) REVERT: A 461 LEU cc_start: -0.0666 (OUTLIER) cc_final: -0.1010 (tp) REVERT: A 524 VAL cc_start: 0.0302 (OUTLIER) cc_final: 0.0080 (t) REVERT: A 794 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7692 (tp) REVERT: A 921 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8062 (mptt) REVERT: A 957 GLN cc_start: 0.8388 (tp-100) cc_final: 0.7996 (tt0) REVERT: A 988 GLU cc_start: 0.8125 (mp0) cc_final: 0.7395 (mp0) REVERT: B 205 SER cc_start: 0.8448 (m) cc_final: 0.8001 (p) REVERT: B 237 ARG cc_start: 0.7143 (mtp85) cc_final: 0.6847 (mtm180) REVERT: B 280 ASN cc_start: 0.7994 (t0) cc_final: 0.7501 (t0) REVERT: B 323 THR cc_start: 0.7180 (p) cc_final: 0.6925 (t) REVERT: B 762 GLN cc_start: 0.8329 (mt0) cc_final: 0.8019 (mt0) REVERT: B 787 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8525 (mt0) REVERT: B 855 PHE cc_start: 0.7475 (m-80) cc_final: 0.7248 (m-80) REVERT: B 867 ASP cc_start: 0.8086 (p0) cc_final: 0.7711 (m-30) REVERT: B 1045 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8361 (tptp) REVERT: C 28 TYR cc_start: 0.7825 (m-80) cc_final: 0.7599 (m-80) REVERT: C 63 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.7991 (m) REVERT: C 190 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.6110 (mtt-85) REVERT: C 675 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: C 755 GLN cc_start: 0.8531 (mp10) cc_final: 0.7849 (mt0) REVERT: C 776 LYS cc_start: 0.8789 (tttm) cc_final: 0.8278 (tttm) REVERT: C 787 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: C 794 ILE cc_start: 0.8215 (mp) cc_final: 0.8012 (tp) REVERT: H 83 MET cc_start: -0.1099 (ttm) cc_final: -0.1335 (ttp) REVERT: H 86 LEU cc_start: -0.1628 (OUTLIER) cc_final: -0.2641 (pt) REVERT: M 67 SER cc_start: 0.4709 (m) cc_final: 0.4269 (p) REVERT: M 78 LEU cc_start: 0.1921 (OUTLIER) cc_final: 0.1366 (tt) REVERT: J 98 ILE cc_start: 0.1570 (OUTLIER) cc_final: 0.1289 (mt) outliers start: 149 outliers final: 75 residues processed: 293 average time/residue: 0.4737 time to fit residues: 172.1467 Evaluate side-chains 238 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 147 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 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 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 A residue 1136 THR Chi-restraints excluded: chain B residue 36 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 523 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 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 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU 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 190 ARG 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 569 ILE 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 608 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR 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 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 70 ILE 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 51 THR Chi-restraints excluded: chain L residue 72 THR 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 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 16 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 25 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 314 GLN B1106 GLN C 188 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN M 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.226081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.140293 restraints weight = 41314.991| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.88 r_work: 0.3091 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30321 Z= 0.142 Angle : 0.675 14.440 41401 Z= 0.327 Chirality : 0.049 0.545 4829 Planarity : 0.004 0.053 5223 Dihedral : 7.705 58.656 5465 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.63 % Favored : 92.17 % Rotamer: Outliers : 5.00 % Allowed : 20.53 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.13), residues: 3589 helix: 0.82 (0.21), residues: 669 sheet: -0.46 (0.16), residues: 1010 loop : -2.43 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.021 0.001 TYR A1067 PHE 0.023 0.001 PHE I 53 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00333 (30205) covalent geometry : angle 0.64873 (41098) SS BOND : bond 0.00415 ( 45) SS BOND : angle 1.55621 ( 90) hydrogen bonds : bond 0.04168 ( 968) hydrogen bonds : angle 5.26667 ( 2682) link_BETA1-4 : bond 0.00622 ( 23) link_BETA1-4 : angle 2.14131 ( 69) link_NAG-ASN : bond 0.00339 ( 48) link_NAG-ASN : angle 2.71186 ( 144) *********************** 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 317 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 158 time to evaluate : 0.783 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: 0.5636 (OUTLIER) cc_final: 0.5353 (m) REVERT: A 233 ILE cc_start: 0.5038 (OUTLIER) cc_final: 0.4828 (pt) REVERT: A 281 GLU cc_start: 0.8077 (pt0) cc_final: 0.7728 (pm20) REVERT: A 309 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: A 331 ASN cc_start: 0.5545 (OUTLIER) cc_final: 0.4808 (m-40) REVERT: A 336 CYS cc_start: 0.0085 (OUTLIER) cc_final: -0.0465 (t) REVERT: A 461 LEU cc_start: -0.0157 (OUTLIER) cc_final: -0.0553 (tp) REVERT: A 583 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: A 794 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7761 (tp) REVERT: A 931 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8587 (mm) REVERT: A 957 GLN cc_start: 0.8239 (tp-100) cc_final: 0.7835 (tt0) REVERT: A 988 GLU cc_start: 0.8217 (mp0) cc_final: 0.7451 (mp0) REVERT: B 66 HIS cc_start: 0.4016 (OUTLIER) cc_final: 0.2646 (m90) REVERT: B 205 SER cc_start: 0.8200 (m) cc_final: 0.7737 (p) REVERT: B 237 ARG cc_start: 0.7135 (mtp85) cc_final: 0.6873 (mtm180) REVERT: B 280 ASN cc_start: 0.7930 (t0) cc_final: 0.7464 (t0) REVERT: B 323 THR cc_start: 0.6829 (p) cc_final: 0.6559 (t) REVERT: B 357 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6527 (mmp-170) REVERT: B 396 TYR cc_start: 0.4966 (m-80) cc_final: 0.4750 (m-80) REVERT: B 552 LEU cc_start: 0.8007 (mt) cc_final: 0.7713 (mm) REVERT: B 569 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7422 (tp) REVERT: B 762 GLN cc_start: 0.8182 (mt0) cc_final: 0.7858 (mt0) REVERT: B 787 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8488 (mt0) REVERT: B 811 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.6165 (mptt) REVERT: B 855 PHE cc_start: 0.7303 (m-80) cc_final: 0.7094 (m-80) REVERT: B 969 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8736 (m110) REVERT: B 1045 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8318 (tptp) REVERT: C 44 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8030 (mtt90) REVERT: C 63 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7915 (m) REVERT: C 190 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5856 (mtt180) REVERT: C 675 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6467 (mp10) REVERT: C 755 GLN cc_start: 0.8420 (mp10) cc_final: 0.7870 (mt0) REVERT: C 776 LYS cc_start: 0.8751 (tttm) cc_final: 0.8249 (tttm) REVERT: C 786 LYS cc_start: 0.8512 (mptt) cc_final: 0.8229 (pttm) REVERT: C 947 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8592 (ttpt) REVERT: I 70 ILE cc_start: 0.1145 (OUTLIER) cc_final: 0.0844 (tp) REVERT: M 46 LEU cc_start: 0.3567 (OUTLIER) cc_final: 0.2954 (tm) REVERT: M 78 LEU cc_start: 0.2717 (OUTLIER) cc_final: 0.1953 (tt) REVERT: J 98 ILE cc_start: 0.1846 (OUTLIER) cc_final: 0.1534 (mt) outliers start: 159 outliers final: 80 residues processed: 299 average time/residue: 0.4792 time to fit residues: 177.4056 Evaluate side-chains 249 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 144 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 277 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 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 794 ILE Chi-restraints excluded: chain A residue 826 VAL 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 994 ASP Chi-restraints excluded: chain A residue 1045 LYS 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 B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR 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 357 ARG 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 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 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU 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 44 ARG 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 190 ARG Chi-restraints excluded: chain C residue 227 VAL 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 533 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 569 ILE 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 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 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 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 70 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 235 optimal weight: 4.9990 chunk 129 optimal weight: 30.0000 chunk 170 optimal weight: 0.0030 chunk 338 optimal weight: 40.0000 chunk 171 optimal weight: 0.9990 chunk 302 optimal weight: 0.0050 chunk 232 optimal weight: 50.0000 chunk 177 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 292 optimal weight: 0.6980 chunk 215 optimal weight: 9.9990 overall best weight: 0.5206 ------------------------------------------------------------------------------- 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 314 GLN B 913 GLN B1106 GLN C 188 ASN C 957 GLN C 960 ASN I 31 HIS 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 = 0.4619 r_free = 0.4619 target = 0.223348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.140722 restraints weight = 41851.257| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 4.17 r_work: 0.3182 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 30321 Z= 0.109 Angle : 0.657 16.437 41401 Z= 0.315 Chirality : 0.050 1.110 4829 Planarity : 0.004 0.051 5223 Dihedral : 7.381 58.846 5459 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.46 % Favored : 93.37 % Rotamer: Outliers : 4.31 % Allowed : 21.88 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 3589 helix: 1.14 (0.21), residues: 666 sheet: -0.31 (0.16), residues: 1007 loop : -2.29 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.018 0.001 TYR A1067 PHE 0.023 0.001 PHE I 53 TRP 0.013 0.001 TRP C 104 HIS 0.002 0.000 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00232 (30205) covalent geometry : angle 0.62936 (41098) SS BOND : bond 0.00451 ( 45) SS BOND : angle 1.44923 ( 90) hydrogen bonds : bond 0.03553 ( 968) hydrogen bonds : angle 5.06561 ( 2682) link_BETA1-4 : bond 0.00566 ( 23) link_BETA1-4 : angle 1.97581 ( 69) link_NAG-ASN : bond 0.00372 ( 48) link_NAG-ASN : angle 2.81095 ( 144) *********************** 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 291 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 154 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.5556 (OUTLIER) cc_final: 0.5330 (m) REVERT: A 233 ILE cc_start: 0.5030 (OUTLIER) cc_final: 0.4808 (pt) REVERT: A 281 GLU cc_start: 0.8065 (pt0) cc_final: 0.7745 (pm20) REVERT: A 309 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: A 329 PHE cc_start: 0.6242 (OUTLIER) cc_final: 0.5194 (m-80) REVERT: A 331 ASN cc_start: 0.5587 (OUTLIER) cc_final: 0.4818 (m-40) REVERT: A 336 CYS cc_start: 0.0359 (OUTLIER) cc_final: -0.0231 (t) REVERT: A 461 LEU cc_start: -0.0339 (OUTLIER) cc_final: -0.0654 (tp) REVERT: A 583 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: A 762 GLN cc_start: 0.8692 (mt0) cc_final: 0.8333 (mt0) REVERT: A 794 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7699 (tp) REVERT: A 931 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8529 (mm) REVERT: A 935 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: A 957 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7972 (tt0) REVERT: A 988 GLU cc_start: 0.8251 (mp0) cc_final: 0.7459 (mp0) REVERT: A 1138 TYR cc_start: 0.8338 (t80) cc_final: 0.8052 (t80) REVERT: B 66 HIS cc_start: 0.4005 (OUTLIER) cc_final: 0.2667 (m90) REVERT: B 205 SER cc_start: 0.8339 (m) cc_final: 0.7886 (p) REVERT: B 280 ASN cc_start: 0.8082 (t0) cc_final: 0.7617 (t0) REVERT: B 323 THR cc_start: 0.6892 (p) cc_final: 0.6616 (t) REVERT: B 396 TYR cc_start: 0.4839 (m-80) cc_final: 0.4629 (m-80) REVERT: B 552 LEU cc_start: 0.8228 (mt) cc_final: 0.8013 (mm) REVERT: B 762 GLN cc_start: 0.8311 (mt0) cc_final: 0.8031 (mt0) REVERT: B 787 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8558 (mt0) REVERT: B 855 PHE cc_start: 0.7308 (m-80) cc_final: 0.7104 (m-80) REVERT: B 969 ASN cc_start: 0.9298 (OUTLIER) cc_final: 0.8934 (m110) REVERT: B 1045 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8331 (tptp) REVERT: C 44 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8131 (mtt90) REVERT: C 63 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7829 (m) REVERT: C 190 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6247 (mtt180) REVERT: C 546 LEU cc_start: 0.6756 (tp) cc_final: 0.6287 (pp) REVERT: C 675 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6469 (mp10) REVERT: C 755 GLN cc_start: 0.8559 (mp10) cc_final: 0.8024 (mt0) REVERT: C 776 LYS cc_start: 0.8854 (tttm) cc_final: 0.8346 (tttm) REVERT: C 786 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8365 (pttm) REVERT: C 796 ASP cc_start: 0.8269 (t0) cc_final: 0.7158 (p0) REVERT: C 947 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8673 (ttpt) REVERT: H 86 LEU cc_start: -0.1182 (OUTLIER) cc_final: -0.2389 (pt) REVERT: I 70 ILE cc_start: 0.1006 (OUTLIER) cc_final: 0.0682 (tp) REVERT: M 46 LEU cc_start: 0.3549 (OUTLIER) cc_final: 0.2904 (tm) REVERT: M 78 LEU cc_start: 0.2453 (OUTLIER) cc_final: 0.1704 (tp) REVERT: J 98 ILE cc_start: 0.1954 (OUTLIER) cc_final: 0.1679 (mt) outliers start: 137 outliers final: 71 residues processed: 273 average time/residue: 0.4607 time to fit residues: 155.7845 Evaluate side-chains 239 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 142 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 277 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 329 PHE 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 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 935 GLN 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 A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 302 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 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 878 LEU Chi-restraints excluded: chain B residue 935 GLN 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 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 44 ARG 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 189 LEU Chi-restraints excluded: chain C residue 190 ARG 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 518 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 569 ILE 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 608 VAL 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 786 LYS 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 1129 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 276 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 312 optimal weight: 30.0000 chunk 338 optimal weight: 30.0000 chunk 245 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 955 ASN B 314 GLN B 334 ASN B 913 GLN B1106 GLN C 314 GLN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN L 27 GLN I 99 HIS J 39 GLN J 99 HIS ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 GLN N 38 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.220616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.138737 restraints weight = 41413.350| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 5.58 r_work: 0.3019 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.125 30321 Z= 0.356 Angle : 0.838 15.131 41401 Z= 0.409 Chirality : 0.057 0.666 4829 Planarity : 0.006 0.055 5223 Dihedral : 7.876 59.778 5454 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.80 % Favored : 91.06 % Rotamer: Outliers : 5.09 % Allowed : 21.38 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.13), residues: 3589 helix: 0.33 (0.20), residues: 670 sheet: -0.50 (0.16), residues: 972 loop : -2.36 (0.12), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1039 TYR 0.031 0.002 TYR A1067 PHE 0.030 0.003 PHE C 86 TRP 0.017 0.002 TRP M 94 HIS 0.010 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00886 (30205) covalent geometry : angle 0.80813 (41098) SS BOND : bond 0.00651 ( 45) SS BOND : angle 2.03985 ( 90) hydrogen bonds : bond 0.06287 ( 968) hydrogen bonds : angle 5.75937 ( 2682) link_BETA1-4 : bond 0.00505 ( 23) link_BETA1-4 : angle 2.36657 ( 69) link_NAG-ASN : bond 0.00456 ( 48) link_NAG-ASN : angle 3.20617 ( 144) *********************** 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 303 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 141 time to evaluate : 1.036 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: 0.5928 (OUTLIER) cc_final: 0.5697 (m) REVERT: A 281 GLU cc_start: 0.8320 (pt0) cc_final: 0.7968 (pm20) REVERT: A 331 ASN cc_start: 0.5378 (OUTLIER) cc_final: 0.4533 (m-40) REVERT: A 336 CYS cc_start: 0.0690 (OUTLIER) cc_final: 0.0084 (t) REVERT: A 461 LEU cc_start: 0.0045 (OUTLIER) cc_final: -0.0415 (tp) REVERT: A 580 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6779 (mm-40) REVERT: A 988 GLU cc_start: 0.8223 (mp0) cc_final: 0.7469 (mp0) REVERT: A 1138 TYR cc_start: 0.8444 (t80) cc_final: 0.8180 (t80) REVERT: B 66 HIS cc_start: 0.4261 (OUTLIER) cc_final: 0.2875 (m90) REVERT: B 205 SER cc_start: 0.8227 (m) cc_final: 0.7862 (p) REVERT: B 233 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.6005 (tp) REVERT: B 280 ASN cc_start: 0.7802 (t0) cc_final: 0.7334 (t0) REVERT: B 319 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8186 (mtp180) REVERT: B 396 TYR cc_start: 0.5038 (m-80) cc_final: 0.4828 (m-80) REVERT: B 569 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7486 (tp) REVERT: B 762 GLN cc_start: 0.8374 (mt0) cc_final: 0.8059 (mt0) REVERT: B 787 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: B 811 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6002 (mtpm) REVERT: B 855 PHE cc_start: 0.7530 (m-80) cc_final: 0.7183 (m-80) REVERT: B 969 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.8995 (m110) REVERT: B 1045 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8472 (tptp) REVERT: C 190 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6278 (mtt-85) REVERT: C 324 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: C 755 GLN cc_start: 0.8411 (mp10) cc_final: 0.7873 (mt0) REVERT: C 776 LYS cc_start: 0.8782 (tttm) cc_final: 0.8519 (ttpp) REVERT: C 786 LYS cc_start: 0.8622 (mptt) cc_final: 0.8092 (pttm) REVERT: C 787 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.7670 (mp10) REVERT: C 796 ASP cc_start: 0.8282 (t0) cc_final: 0.7328 (p0) REVERT: C 947 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8674 (ttpt) REVERT: C 990 GLU cc_start: 0.8008 (tt0) cc_final: 0.7784 (mp0) REVERT: L 27 GLN cc_start: 0.0702 (OUTLIER) cc_final: -0.0132 (mt0) REVERT: I 70 ILE cc_start: 0.0723 (OUTLIER) cc_final: 0.0448 (tp) REVERT: M 4 MET cc_start: 0.2642 (mmp) cc_final: 0.2282 (mtt) REVERT: M 46 LEU cc_start: 0.3500 (OUTLIER) cc_final: 0.2787 (tm) REVERT: M 78 LEU cc_start: 0.3065 (OUTLIER) cc_final: 0.2023 (tp) REVERT: J 98 ILE cc_start: 0.1933 (OUTLIER) cc_final: 0.1617 (mt) REVERT: J 114 GLN cc_start: 0.2998 (OUTLIER) cc_final: 0.1849 (tt0) outliers start: 162 outliers final: 86 residues processed: 288 average time/residue: 0.4749 time to fit residues: 169.2663 Evaluate side-chains 235 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 126 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 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 580 GLN 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 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 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 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU 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 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 705 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 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 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 190 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 315 THR 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 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 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE 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 931 ILE Chi-restraints excluded: chain C residue 947 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 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 GLN 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 J residue 114 GLN Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 264 optimal weight: 4.9990 chunk 266 optimal weight: 0.3980 chunk 349 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 323 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 197 optimal weight: 6.9990 chunk 190 optimal weight: 0.7980 chunk 324 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 314 GLN B 703 ASN B1106 GLN C 121 ASN ** C 188 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 = 0.4642 r_free = 0.4642 target = 0.226990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.149036 restraints weight = 43171.368| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 4.28 r_work: 0.3407 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30321 Z= 0.119 Angle : 0.676 12.542 41401 Z= 0.327 Chirality : 0.049 0.550 4829 Planarity : 0.004 0.053 5223 Dihedral : 7.213 59.513 5451 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.35 % Favored : 93.48 % Rotamer: Outliers : 3.30 % Allowed : 22.98 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 3589 helix: 1.08 (0.21), residues: 662 sheet: -0.32 (0.16), residues: 1011 loop : -2.26 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 646 TYR 0.016 0.001 TYR C1067 PHE 0.024 0.001 PHE J 53 TRP 0.013 0.001 TRP C 104 HIS 0.002 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00257 (30205) covalent geometry : angle 0.65274 (41098) SS BOND : bond 0.00404 ( 45) SS BOND : angle 1.51328 ( 90) hydrogen bonds : bond 0.03974 ( 968) hydrogen bonds : angle 5.27220 ( 2682) link_BETA1-4 : bond 0.00628 ( 23) link_BETA1-4 : angle 1.96268 ( 69) link_NAG-ASN : bond 0.00402 ( 48) link_NAG-ASN : angle 2.57725 ( 144) *********************** 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 250 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 145 time to evaluate : 1.154 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 281 GLU cc_start: 0.8345 (pt0) cc_final: 0.8092 (pm20) REVERT: A 331 ASN cc_start: 0.5767 (OUTLIER) cc_final: 0.4934 (m-40) REVERT: A 336 CYS cc_start: 0.0382 (OUTLIER) cc_final: -0.0221 (t) REVERT: A 461 LEU cc_start: -0.0572 (OUTLIER) cc_final: -0.0819 (tp) REVERT: A 541 PHE cc_start: 0.7539 (p90) cc_final: 0.7215 (p90) REVERT: A 957 GLN cc_start: 0.8343 (tp-100) cc_final: 0.7976 (tt0) REVERT: A 988 GLU cc_start: 0.8328 (mp0) cc_final: 0.7552 (mp0) REVERT: A 1138 TYR cc_start: 0.8452 (t80) cc_final: 0.8184 (t80) REVERT: B 66 HIS cc_start: 0.4288 (OUTLIER) cc_final: 0.2888 (m90) REVERT: B 189 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6549 (mp) REVERT: B 205 SER cc_start: 0.8457 (m) cc_final: 0.8209 (p) REVERT: B 226 LEU cc_start: 0.5820 (tp) cc_final: 0.5547 (pp) REVERT: B 227 VAL cc_start: 0.7792 (t) cc_final: 0.7296 (m) REVERT: B 280 ASN cc_start: 0.8036 (t0) cc_final: 0.7624 (t0) REVERT: B 524 VAL cc_start: 0.6138 (OUTLIER) cc_final: 0.5851 (p) REVERT: B 762 GLN cc_start: 0.8344 (mt0) cc_final: 0.8054 (mt0) REVERT: B 787 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8634 (mt0) REVERT: B 855 PHE cc_start: 0.7340 (m-80) cc_final: 0.7109 (m-80) REVERT: B 1045 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8374 (tptp) REVERT: C 546 LEU cc_start: 0.7151 (tp) cc_final: 0.6631 (pp) REVERT: C 755 GLN cc_start: 0.8488 (mp10) cc_final: 0.8044 (mt0) REVERT: C 776 LYS cc_start: 0.8830 (tttm) cc_final: 0.8318 (tttm) REVERT: C 786 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8344 (pttm) REVERT: M 46 LEU cc_start: 0.3772 (OUTLIER) cc_final: 0.2888 (tm) REVERT: M 78 LEU cc_start: 0.2149 (OUTLIER) cc_final: 0.1457 (tp) REVERT: J 98 ILE cc_start: 0.1879 (OUTLIER) cc_final: 0.1577 (mt) outliers start: 105 outliers final: 69 residues processed: 235 average time/residue: 0.4658 time to fit residues: 136.6315 Evaluate side-chains 216 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 135 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 620 VAL 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 937 SER Chi-restraints excluded: chain A residue 951 VAL 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 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ARG 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 791 THR 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 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 213 VAL 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 533 LEU 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 608 VAL 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 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 70 ILE 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 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 86 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 51 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 205 optimal weight: 7.9990 chunk 202 optimal weight: 0.3980 chunk 214 optimal weight: 5.9990 chunk 280 optimal weight: 7.9990 chunk 138 optimal weight: 30.0000 chunk 274 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 314 GLN B 703 ASN B1106 GLN C 580 GLN C 960 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4639 r_free = 0.4639 target = 0.226075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.149309 restraints weight = 43324.118| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.09 r_work: 0.3465 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30321 Z= 0.126 Angle : 0.659 12.162 41401 Z= 0.318 Chirality : 0.048 0.509 4829 Planarity : 0.004 0.055 5223 Dihedral : 6.830 58.947 5448 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.22 % Favored : 92.62 % Rotamer: Outliers : 3.62 % Allowed : 22.85 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3589 helix: 1.29 (0.21), residues: 664 sheet: -0.20 (0.16), residues: 1003 loop : -2.20 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 646 TYR 0.019 0.001 TYR C1067 PHE 0.023 0.001 PHE J 53 TRP 0.010 0.001 TRP A 436 HIS 0.007 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00287 (30205) covalent geometry : angle 0.63738 (41098) SS BOND : bond 0.00402 ( 45) SS BOND : angle 1.44007 ( 90) hydrogen bonds : bond 0.03904 ( 968) hydrogen bonds : angle 5.10297 ( 2682) link_BETA1-4 : bond 0.00539 ( 23) link_BETA1-4 : angle 1.93617 ( 69) link_NAG-ASN : bond 0.00345 ( 48) link_NAG-ASN : angle 2.44851 ( 144) *********************** 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 251 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 136 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8339 (pt0) cc_final: 0.8109 (pm20) REVERT: A 331 ASN cc_start: 0.5847 (OUTLIER) cc_final: 0.5079 (m-40) REVERT: A 541 PHE cc_start: 0.7582 (p90) cc_final: 0.7334 (p90) REVERT: A 794 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7889 (tp) REVERT: A 957 GLN cc_start: 0.8339 (tp-100) cc_final: 0.7954 (tt0) REVERT: A 988 GLU cc_start: 0.8321 (mp0) cc_final: 0.7582 (mp0) REVERT: A 1138 TYR cc_start: 0.8407 (t80) cc_final: 0.8157 (t80) REVERT: B 66 HIS cc_start: 0.4315 (OUTLIER) cc_final: 0.2915 (m90) REVERT: B 189 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6489 (mp) REVERT: B 205 SER cc_start: 0.8383 (m) cc_final: 0.8139 (p) REVERT: B 226 LEU cc_start: 0.6191 (tp) cc_final: 0.5936 (pp) REVERT: B 227 VAL cc_start: 0.7816 (t) cc_final: 0.7258 (m) REVERT: B 233 ILE cc_start: 0.6145 (OUTLIER) cc_final: 0.5844 (tp) REVERT: B 280 ASN cc_start: 0.8064 (t0) cc_final: 0.7666 (t0) REVERT: B 357 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.7018 (mmp-170) REVERT: B 524 VAL cc_start: 0.6376 (OUTLIER) cc_final: 0.6084 (p) REVERT: B 552 LEU cc_start: 0.8281 (mt) cc_final: 0.8058 (mm) REVERT: B 675 GLN cc_start: 0.7293 (tt0) cc_final: 0.7060 (tm-30) REVERT: B 762 GLN cc_start: 0.8320 (mt0) cc_final: 0.8033 (mt0) REVERT: B 787 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8600 (mt0) REVERT: B 855 PHE cc_start: 0.7330 (m-80) cc_final: 0.7076 (m-80) REVERT: B 1045 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8314 (tptp) REVERT: C 357 ARG cc_start: 0.3653 (OUTLIER) cc_final: 0.1836 (tpp-160) REVERT: C 546 LEU cc_start: 0.7153 (tp) cc_final: 0.6638 (pp) REVERT: C 755 GLN cc_start: 0.8554 (mp10) cc_final: 0.8154 (mt0) REVERT: C 776 LYS cc_start: 0.8825 (tttm) cc_final: 0.8303 (tttm) REVERT: C 786 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8281 (pttm) REVERT: C 947 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8623 (ttpt) REVERT: L 4 MET cc_start: 0.2168 (OUTLIER) cc_final: 0.1436 (ppp) REVERT: I 70 ILE cc_start: 0.0950 (OUTLIER) cc_final: 0.0578 (tp) REVERT: M 46 LEU cc_start: 0.4028 (OUTLIER) cc_final: 0.2997 (tm) REVERT: M 78 LEU cc_start: 0.1566 (OUTLIER) cc_final: 0.0926 (tp) outliers start: 115 outliers final: 75 residues processed: 230 average time/residue: 0.4993 time to fit residues: 141.5994 Evaluate side-chains 225 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 134 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 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 794 ILE 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 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR 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 233 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ARG 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 791 THR 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 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 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 357 ARG 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 533 LEU 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 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 770 ILE 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 988 GLU 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 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 MET 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 86 LEU Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 1 optimal weight: 4.9990 chunk 223 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 314 GLN B 703 ASN B1106 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN M 38 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.225497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.149181 restraints weight = 42878.461| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.09 r_work: 0.3412 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4670 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= 0.248 Angle : 0.752 13.645 41401 Z= 0.365 Chirality : 0.052 0.531 4829 Planarity : 0.005 0.056 5223 Dihedral : 7.230 59.297 5448 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.05 % Favored : 91.75 % Rotamer: Outliers : 3.46 % Allowed : 23.04 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.14), residues: 3589 helix: 0.83 (0.21), residues: 663 sheet: -0.28 (0.17), residues: 980 loop : -2.24 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 190 TYR 0.025 0.002 TYR A1067 PHE 0.031 0.002 PHE C 65 TRP 0.014 0.002 TRP A 436 HIS 0.007 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00613 (30205) covalent geometry : angle 0.72597 (41098) SS BOND : bond 0.00519 ( 45) SS BOND : angle 1.91324 ( 90) hydrogen bonds : bond 0.05368 ( 968) hydrogen bonds : angle 5.48481 ( 2682) link_BETA1-4 : bond 0.00526 ( 23) link_BETA1-4 : angle 2.14071 ( 69) link_NAG-ASN : bond 0.00356 ( 48) link_NAG-ASN : angle 2.73987 ( 144) ********************** 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 241 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 131 time to evaluate : 1.091 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 200 TYR cc_start: 0.7638 (m-80) cc_final: 0.7278 (m-80) REVERT: A 281 GLU cc_start: 0.8421 (pt0) cc_final: 0.8179 (pm20) REVERT: A 331 ASN cc_start: 0.5860 (OUTLIER) cc_final: 0.5133 (m-40) REVERT: A 988 GLU cc_start: 0.8271 (mp0) cc_final: 0.7550 (mp0) REVERT: A 1138 TYR cc_start: 0.8558 (t80) cc_final: 0.8332 (t80) REVERT: B 66 HIS cc_start: 0.4392 (OUTLIER) cc_final: 0.2962 (m90) REVERT: B 205 SER cc_start: 0.8530 (m) cc_final: 0.8092 (p) REVERT: B 233 ILE cc_start: 0.6358 (OUTLIER) cc_final: 0.6034 (tp) REVERT: B 280 ASN cc_start: 0.7943 (t0) cc_final: 0.7491 (t0) REVERT: B 675 GLN cc_start: 0.7537 (tt0) cc_final: 0.7292 (tm-30) REVERT: B 762 GLN cc_start: 0.8455 (mt0) cc_final: 0.8166 (mt0) REVERT: B 787 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8631 (mt0) REVERT: B 855 PHE cc_start: 0.7502 (m-80) cc_final: 0.7244 (m-80) REVERT: B 1045 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8451 (tptp) REVERT: C 357 ARG cc_start: 0.3986 (OUTLIER) cc_final: 0.1874 (tpp-160) REVERT: C 755 GLN cc_start: 0.8597 (mp10) cc_final: 0.8140 (mt0) REVERT: C 776 LYS cc_start: 0.8883 (tttm) cc_final: 0.8369 (tttm) REVERT: C 786 LYS cc_start: 0.8677 (mptt) cc_final: 0.8349 (pttm) REVERT: C 947 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8738 (ttpt) REVERT: L 4 MET cc_start: 0.2591 (OUTLIER) cc_final: 0.1865 (ppp) REVERT: I 70 ILE cc_start: 0.0739 (OUTLIER) cc_final: 0.0390 (tp) REVERT: M 46 LEU cc_start: 0.4229 (OUTLIER) cc_final: 0.3192 (tm) REVERT: M 78 LEU cc_start: 0.1556 (OUTLIER) cc_final: 0.1000 (tp) outliers start: 110 outliers final: 75 residues processed: 229 average time/residue: 0.4792 time to fit residues: 136.5049 Evaluate side-chains 210 residues out of total 3181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 124 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 549 THR 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 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 985 ASP 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 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 233 ILE Chi-restraints excluded: chain B residue 357 ARG 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 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 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 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 357 ARG 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 533 LEU 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 608 VAL Chi-restraints excluded: chain C residue 649 CYS 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 4 MET 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 86 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 257 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 333 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 242 optimal weight: 0.3980 chunk 303 optimal weight: 20.0000 chunk 362 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 121 ASN B 314 GLN B 703 ASN B1106 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN M 38 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.226807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.150205 restraints weight = 43092.388| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 4.83 r_work: 0.3426 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30321 Z= 0.136 Angle : 0.673 11.971 41401 Z= 0.325 Chirality : 0.048 0.514 4829 Planarity : 0.004 0.058 5223 Dihedral : 6.854 57.424 5447 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.83 % Favored : 93.01 % Rotamer: Outliers : 2.89 % Allowed : 23.61 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.14), residues: 3589 helix: 1.20 (0.21), residues: 663 sheet: -0.15 (0.17), residues: 984 loop : -2.16 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 646 TYR 0.019 0.001 TYR C1067 PHE 0.023 0.001 PHE J 53 TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00317 (30205) covalent geometry : angle 0.65196 (41098) SS BOND : bond 0.00402 ( 45) SS BOND : angle 1.51009 ( 90) hydrogen bonds : bond 0.04046 ( 968) hydrogen bonds : angle 5.17978 ( 2682) link_BETA1-4 : bond 0.00537 ( 23) link_BETA1-4 : angle 1.94523 ( 69) link_NAG-ASN : bond 0.00328 ( 48) link_NAG-ASN : angle 2.41154 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15157.92 seconds wall clock time: 257 minutes 15.23 seconds (15435.23 seconds total)