Starting phenix.real_space_refine on Sun Jul 5 22:41:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7epx_31249/07_2026/7epx_31249.cif Found real_map, /net/cci-nas-00/data/ceres_data/7epx_31249/07_2026/7epx_31249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7epx_31249/07_2026/7epx_31249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7epx_31249/07_2026/7epx_31249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7epx_31249/07_2026/7epx_31249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7epx_31249/07_2026/7epx_31249.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7epx_31249/07_2026/7epx_31249.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7epx_31249/07_2026/7epx_31249.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 128 5.16 5 C 19542 2.51 5 N 5052 2.21 5 O 6124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30846 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 53, 'TRANS': 953} Chain breaks: 8 Chain: "B" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 53, 'TRANS': 952} Chain breaks: 8 Chain: "C" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 51, 'TRANS': 919} Chain breaks: 9 Chain: "H" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1701 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 13, 'TRANS': 214} Chain: "L" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1564 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "I" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1701 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 13, 'TRANS': 214} Chain: "M" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1564 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} 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 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 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 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 6.26, per 1000 atoms: 0.20 Number of scatterers: 30846 At special positions: 0 Unit cell: (189.138, 173.92, 194.573, 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 128 16.00 O 6124 8.00 N 5052 7.00 C 19542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.08 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.15 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.96 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 H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 137 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 137 " - pdb=" SG CYS M 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 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 J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN B1074 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7192 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 63 sheets defined 19.9% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.064A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.567A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A 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: 3.773A 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: 3.641A 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: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.773A 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: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A 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: 3.649A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.577A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.864A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A 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 337 through 341 removed outlier: 4.064A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.568A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 438 through 443 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: 3.631A 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: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.650A 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 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A 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: 3.565A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.246A 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: 3.673A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A 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 364 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.568A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.716A 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: 3.699A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.634A 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: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.623A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.554A 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: 3.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A 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: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'L' and resid 124 through 130 Processing helix chain 'L' and resid 184 through 191 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 201 through 203 No H-bonds generated for 'chain 'I' and resid 201 through 203' Processing helix chain 'M' and resid 124 through 130 Processing helix chain 'M' and resid 184 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A 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: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A 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: 3.730A 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: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.081A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.620A 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 358 removed outlier: 3.871A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (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 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.720A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A 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=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A 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: 3.976A 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: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, 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=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.679A 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: 4.438A 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=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A 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: 4.586A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.369A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.339A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.871A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.292A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, 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: 6.525A 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: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, 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: 6.525A 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: 6.211A 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=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A 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: 4.438A 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=AD5, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A 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: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A 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) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 319 removed outlier: 6.141A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 327 removed outlier: 4.026A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.659A 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=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.871A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.608A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A 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: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A 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: 6.147A 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: 3.880A 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=AE6, 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=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.197A pdb=" N GLY H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.008A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.008A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 164 through 168 Processing sheet with id=AF4, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AF5, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.370A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN L 35 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 117 through 121 Processing sheet with id=AF7, first strand: chain 'L' and resid 117 through 121 Processing sheet with id=AF8, first strand: chain 'L' and resid 157 through 158 removed outlier: 4.439A pdb=" N TRP L 151 " --> pdb=" O VAL L 158 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.197A pdb=" N GLY I 10 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA I 151 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL I 198 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 153 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 196 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 155 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 194 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 157 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 192 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA I 151 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL I 198 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 153 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 196 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 155 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 194 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 157 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 192 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 164 through 168 Processing sheet with id=AG5, first strand: chain 'M' and resid 17 through 23 Processing sheet with id=AG6, first strand: chain 'M' and resid 46 through 49 removed outlier: 6.370A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN M 35 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 117 through 121 Processing sheet with id=AG8, first strand: chain 'M' and resid 117 through 121 Processing sheet with id=AG9, first strand: chain 'M' and resid 157 through 158 removed outlier: 4.440A pdb=" N TRP M 151 " --> pdb=" O VAL M 158 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3108 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: 8.12 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8179 1.33 - 1.46: 8454 1.46 - 1.58: 14739 1.58 - 1.71: 0 1.71 - 1.84: 161 Bond restraints: 31533 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=" C ASP A 985 " pdb=" N PRO A 986 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.18e-02 7.18e+03 2.57e+01 bond pdb=" C GLN C 321 " pdb=" N PRO C 322 " ideal model delta sigma weight residual 1.331 1.390 -0.060 1.31e-02 5.83e+03 2.08e+01 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.23e-02 6.61e+03 1.89e+01 bond pdb=" N PRO A 986 " pdb=" CD PRO A 986 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 ... (remaining 31528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 41817 2.74 - 5.48: 1024 5.48 - 8.22: 72 8.22 - 10.96: 6 10.96 - 13.70: 8 Bond angle restraints: 42927 Sorted by residual: angle pdb=" C ASP A 985 " pdb=" N PRO A 986 " pdb=" CA PRO A 986 " ideal model delta sigma weight residual 120.38 114.09 6.29 1.03e+00 9.43e-01 3.72e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C GLN C 321 " pdb=" N PRO C 322 " pdb=" CA PRO C 322 " ideal model delta sigma weight residual 119.85 114.08 5.77 1.01e+00 9.80e-01 3.27e+01 ... (remaining 42922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15660 17.93 - 35.86: 1891 35.86 - 53.79: 520 53.79 - 71.72: 128 71.72 - 89.65: 48 Dihedral angle restraints: 18247 sinusoidal: 7057 harmonic: 11190 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 21.08 71.92 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 21.09 71.91 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 ... (remaining 18244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 5067 0.329 - 0.659: 4 0.659 - 0.988: 5 0.988 - 1.317: 0 1.317 - 1.647: 1 Chirality restraints: 5077 Sorted by residual: chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.02e+03 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 ... (remaining 5074 not shown) Planarity restraints: 5509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.104 2.00e-02 2.50e+03 1.98e-01 4.90e+02 pdb=" CG ASN C 331 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.355 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.141 2.00e-02 2.50e+03 1.67e-01 3.49e+02 pdb=" CG ASN B 331 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.278 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.131 2.00e-02 2.50e+03 1.61e-01 3.23e+02 pdb=" CG ASN A 331 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.270 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.192 2.00e-02 2.50e+03 ... (remaining 5506 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 315 2.53 - 3.12: 23040 3.12 - 3.71: 45182 3.71 - 4.31: 66002 4.31 - 4.90: 109745 Nonbonded interactions: 244284 Sorted by model distance: nonbonded pdb=" O VAL H 125 " pdb=" OG SER H 126 " model vdw 1.934 3.040 nonbonded pdb=" O VAL I 125 " pdb=" OG SER I 126 " model vdw 1.934 3.040 nonbonded pdb=" OD1 ASN C 532 " pdb=" N LEU C 533 " model vdw 1.966 3.120 nonbonded pdb=" N GLU B 748 " pdb=" OE1 GLU B 748 " model vdw 2.140 3.120 nonbonded pdb=" O GLY A 700 " pdb=" O ALA A 701 " model vdw 2.167 3.040 ... (remaining 244279 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 455 or resid 491 through 939 or resid 944 throu \ gh 1408)) selection = (chain 'B' and (resid 27 through 455 or resid 491 through 1408)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.020 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 0.194 31650 Z= 0.482 Angle : 1.199 48.921 43232 Z= 0.636 Chirality : 0.072 1.647 5077 Planarity : 0.007 0.090 5461 Dihedral : 17.581 89.648 10917 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 2.40 % Allowed : 10.93 % Favored : 86.68 % Rotamer: Outliers : 10.46 % Allowed : 18.18 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.11), residues: 3798 helix: -2.43 (0.15), residues: 712 sheet: -1.64 (0.14), residues: 1053 loop : -3.36 (0.11), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.028 0.003 TYR B1067 PHE 0.033 0.003 PHE H 29 TRP 0.025 0.003 TRP C 104 HIS 0.010 0.002 HIS H 32 Details of bonding type rmsd/Z covalent geometry : bond 0.01059 / 0.47 (31533) covalent geometry : angle 1.03004 / 0.59 (42927) SS BOND : bond 0.02830 / 2.00 ( 46) SS BOND : angle 8.05020 / 5.57 ( 92) hydrogen bonds : bond 0.18409 / 12.03 ( 1096) hydrogen bonds : angle 7.94373 / 5.40 ( 3108) link_BETA1-4 : bond 0.04239 / 3.14 ( 23) link_BETA1-4 : angle 6.09256 / 3.89 ( 69) link_NAG-ASN : bond 0.02245 / 1.21 ( 48) link_NAG-ASN : angle 7.49448 / 5.47 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 351 poor density : 359 time to evaluate : 0.929 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 109 THR cc_start: 0.5565 (OUTLIER) cc_final: 0.5314 (m) REVERT: A 143 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6406 (t) REVERT: A 335 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4920 (mp) REVERT: A 983 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7424 (mtm110) REVERT: A 1039 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8890 (mtp180) REVERT: B 109 THR cc_start: 0.6101 (OUTLIER) cc_final: 0.5703 (m) REVERT: B 153 MET cc_start: 0.4251 (mpp) cc_final: 0.2476 (ptt) REVERT: B 164 ASN cc_start: 0.4183 (OUTLIER) cc_final: 0.3169 (m-40) REVERT: B 422 ASN cc_start: 0.0201 (OUTLIER) cc_final: -0.0138 (t0) REVERT: B 950 ASP cc_start: 0.7990 (m-30) cc_final: 0.7786 (m-30) REVERT: C 153 MET cc_start: 0.3196 (mpp) cc_final: 0.1184 (ptp) REVERT: C 158 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.4532 (ttp-170) REVERT: C 218 GLN cc_start: 0.7063 (tt0) cc_final: 0.6668 (tm130) REVERT: C 314 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: C 528 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6511 (mmmm) REVERT: C 529 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6757 (ptmm) REVERT: C 535 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7757 (ttmt) REVERT: H 83 MET cc_start: -0.0818 (mtp) cc_final: -0.1317 (mmm) REVERT: H 114 MET cc_start: 0.0113 (mtm) cc_final: -0.0127 (mtp) REVERT: H 178 HIS cc_start: 0.0303 (OUTLIER) cc_final: -0.0230 (m-70) REVERT: I 102 TYR cc_start: 0.2377 (OUTLIER) cc_final: 0.2136 (p90) REVERT: I 211 ASN cc_start: 0.0918 (OUTLIER) cc_final: 0.0579 (m110) REVERT: M 183 LEU cc_start: 0.0426 (OUTLIER) cc_final: -0.0507 (tp) outliers start: 351 outliers final: 74 residues processed: 654 average time/residue: 0.4744 time to fit residues: 381.1740 Evaluate side-chains 263 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 172 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 183 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 137 ASN A 239 GLN A 450 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 658 ASN A 804 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 960 ASN A 969 ASN A 992 GLN A1011 GLN A1101 HIS B 134 GLN B 137 ASN B 317 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 498 GLN B 644 GLN B 804 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1005 GLN B1054 GLN C 134 GLN C 137 ASN C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN C 703 ASN C 751 ASN C 755 GLN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS L 6 GLN L 38 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN M 6 GLN M 191 HIS ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.207704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.167071 restraints weight = 50680.236| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.90 r_work: 0.3209 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31650 Z= 0.230 Angle : 0.863 15.339 43232 Z= 0.418 Chirality : 0.053 0.516 5077 Planarity : 0.006 0.062 5461 Dihedral : 8.541 97.537 4264 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.85 % Favored : 90.94 % Rotamer: Outliers : 5.63 % Allowed : 21.58 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.12), residues: 3798 helix: -0.47 (0.19), residues: 703 sheet: -1.05 (0.15), residues: 1083 loop : -2.75 (0.12), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1039 TYR 0.031 0.002 TYR A 453 PHE 0.016 0.002 PHE B 898 TRP 0.017 0.002 TRP A 104 HIS 0.007 0.002 HIS M 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (31533) covalent geometry : angle 0.82127 / 0.41 (42927) SS BOND : bond 0.00464 / 0.31 ( 46) SS BOND : angle 2.00905 / 1.27 ( 92) hydrogen bonds : bond 0.05521 / 3.64 ( 1096) hydrogen bonds : angle 6.00674 / 4.15 ( 3108) link_BETA1-4 : bond 0.00811 / 0.42 ( 23) link_BETA1-4 : angle 2.52951 / 1.56 ( 69) link_NAG-ASN : bond 0.00754 / 0.56 ( 48) link_NAG-ASN : angle 4.12291 / 2.76 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 180 time to evaluate : 1.119 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 125 ASN cc_start: 0.3294 (p0) cc_final: 0.2962 (p0) REVERT: A 164 ASN cc_start: 0.4650 (OUTLIER) cc_final: 0.4107 (p0) REVERT: A 237 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6899 (mmm-85) REVERT: A 335 LEU cc_start: 0.5219 (OUTLIER) cc_final: 0.4854 (mp) REVERT: A 546 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.6925 (mm) REVERT: A 1094 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.9040 (t) REVERT: B 153 MET cc_start: 0.4065 (mpp) cc_final: 0.2130 (ptt) REVERT: B 554 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7007 (tp30) REVERT: C 153 MET cc_start: 0.2924 (mpp) cc_final: 0.0729 (ptm) REVERT: C 158 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.4320 (ttt180) REVERT: C 190 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8207 (mtm180) REVERT: C 529 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7539 (tppt) REVERT: C 814 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7271 (mmtt) REVERT: C 1029 MET cc_start: 0.9167 (tpp) cc_final: 0.8921 (tpp) REVERT: H 34 MET cc_start: 0.5287 (mpm) cc_final: 0.4631 (mpm) REVERT: H 83 MET cc_start: -0.1417 (mtp) cc_final: -0.1792 (mmm) REVERT: H 114 MET cc_start: -0.0704 (mtm) cc_final: -0.1016 (mtp) REVERT: H 178 HIS cc_start: 0.0598 (OUTLIER) cc_final: -0.0112 (m-70) REVERT: I 106 ASP cc_start: 0.4172 (OUTLIER) cc_final: 0.3549 (m-30) REVERT: I 184 LEU cc_start: 0.2534 (OUTLIER) cc_final: 0.2162 (pt) REVERT: I 211 ASN cc_start: 0.1555 (OUTLIER) cc_final: 0.0684 (m110) outliers start: 189 outliers final: 69 residues processed: 341 average time/residue: 0.4338 time to fit residues: 186.3803 Evaluate side-chains 226 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 143 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 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 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 558 LYS 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 786 LYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 80 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 366 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.0980 chunk 222 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 690 GLN B1010 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 544 ASN C 969 ASN L 191 HIS ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** 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 = 0.4496 r_free = 0.4496 target = 0.207955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.159579 restraints weight = 49804.801| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.75 r_work: 0.3020 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 31650 Z= 0.237 Angle : 0.814 14.065 43232 Z= 0.390 Chirality : 0.052 0.726 5077 Planarity : 0.005 0.053 5461 Dihedral : 7.034 59.510 4177 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.16 % Favored : 91.68 % Rotamer: Outliers : 6.20 % Allowed : 20.18 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.13), residues: 3798 helix: 0.06 (0.20), residues: 710 sheet: -0.68 (0.15), residues: 1093 loop : -2.47 (0.12), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 72 TYR 0.025 0.002 TYR I 95 PHE 0.025 0.002 PHE A 238 TRP 0.012 0.002 TRP M 98 HIS 0.007 0.002 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (31533) covalent geometry : angle 0.78082 / 0.38 (42927) SS BOND : bond 0.00632 / 0.33 ( 46) SS BOND : angle 1.89844 / 1.23 ( 92) hydrogen bonds : bond 0.05257 / 3.47 ( 1096) hydrogen bonds : angle 5.66405 / 3.91 ( 3108) link_BETA1-4 : bond 0.00502 / 0.26 ( 23) link_BETA1-4 : angle 2.42238 / 1.49 ( 69) link_NAG-ASN : bond 0.00589 / 0.33 ( 48) link_NAG-ASN : angle 3.49492 / 2.30 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 164 time to evaluate : 1.022 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 164 ASN cc_start: 0.4445 (OUTLIER) cc_final: 0.3981 (p0) REVERT: A 190 ARG cc_start: 0.8619 (mtt90) cc_final: 0.8111 (mmm-85) REVERT: A 237 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6549 (mmm-85) REVERT: A 379 CYS cc_start: 0.2333 (OUTLIER) cc_final: 0.1657 (p) REVERT: A 546 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6985 (mm) REVERT: A 855 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.5671 (t80) REVERT: A 869 MET cc_start: 0.9301 (mtt) cc_final: 0.9036 (mtt) REVERT: A 1019 ARG cc_start: 0.9053 (tpt170) cc_final: 0.8805 (ttm110) REVERT: A 1094 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9167 (t) REVERT: B 153 MET cc_start: 0.3728 (mpp) cc_final: 0.1960 (ptt) REVERT: B 544 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7468 (m110) REVERT: B 554 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7275 (tp30) REVERT: C 153 MET cc_start: 0.2363 (mpp) cc_final: -0.0308 (ttm) REVERT: C 190 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8266 (mtm180) REVERT: C 528 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7473 (mmtt) REVERT: C 529 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7516 (tppt) REVERT: C 535 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7705 (ttmt) REVERT: C 558 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6357 (pmmt) REVERT: C 814 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7797 (mmtt) REVERT: H 60 TYR cc_start: 0.2641 (OUTLIER) cc_final: 0.1933 (m-10) REVERT: H 114 MET cc_start: -0.1072 (mtm) cc_final: -0.1636 (mtp) REVERT: H 178 HIS cc_start: 0.0742 (OUTLIER) cc_final: 0.0161 (m-70) REVERT: L 152 LYS cc_start: 0.1514 (OUTLIER) cc_final: 0.1250 (ptpt) REVERT: L 190 SER cc_start: 0.0161 (OUTLIER) cc_final: -0.0229 (m) REVERT: I 83 MET cc_start: 0.2931 (mmp) cc_final: 0.1749 (mtp) REVERT: I 106 ASP cc_start: 0.4262 (OUTLIER) cc_final: 0.3498 (m-30) REVERT: I 184 LEU cc_start: 0.2825 (OUTLIER) cc_final: 0.2180 (pt) REVERT: I 211 ASN cc_start: 0.1587 (OUTLIER) cc_final: 0.0538 (m110) REVERT: M 183 LEU cc_start: -0.0140 (OUTLIER) cc_final: -0.1021 (tp) outliers start: 208 outliers final: 94 residues processed: 341 average time/residue: 0.4481 time to fit residues: 191.9990 Evaluate side-chains 255 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 139 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET 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 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 152 LYS Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 29 optimal weight: 20.0000 chunk 265 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 337 optimal weight: 20.0000 chunk 329 optimal weight: 30.0000 chunk 360 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 192 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 99 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.207782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.160052 restraints weight = 49482.091| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.62 r_work: 0.3072 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31650 Z= 0.133 Angle : 0.723 13.656 43232 Z= 0.343 Chirality : 0.049 0.634 5077 Planarity : 0.005 0.055 5461 Dihedral : 6.358 58.861 4163 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.14 % Favored : 92.71 % Rotamer: Outliers : 5.07 % Allowed : 21.64 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.69 (0.13), residues: 3798 helix: 0.56 (0.20), residues: 711 sheet: -0.41 (0.15), residues: 1083 loop : -2.24 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 158 TYR 0.017 0.001 TYR B1067 PHE 0.019 0.001 PHE A 140 TRP 0.010 0.001 TRP M 36 HIS 0.005 0.001 HIS L 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (31533) covalent geometry : angle 0.69183 / 0.34 (42927) SS BOND : bond 0.00329 / 0.21 ( 46) SS BOND : angle 1.59428 / 1.08 ( 92) hydrogen bonds : bond 0.04060 / 2.69 ( 1096) hydrogen bonds : angle 5.33769 / 3.68 ( 3108) link_BETA1-4 : bond 0.00605 / 0.33 ( 23) link_BETA1-4 : angle 2.27616 / 1.44 ( 69) link_NAG-ASN : bond 0.00713 / 0.40 ( 48) link_NAG-ASN : angle 3.17279 / 2.03 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 151 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.7070 (p90) cc_final: 0.6793 (p90) REVERT: A 190 ARG cc_start: 0.8497 (mtt90) cc_final: 0.7888 (mmm-85) REVERT: A 237 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6476 (mmm-85) REVERT: A 333 THR cc_start: 0.4932 (OUTLIER) cc_final: 0.4665 (t) REVERT: A 335 LEU cc_start: 0.4897 (OUTLIER) cc_final: 0.4663 (mp) REVERT: A 546 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6976 (mm) REVERT: A 855 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.5798 (t80) REVERT: A 1019 ARG cc_start: 0.8999 (tpt170) cc_final: 0.8787 (ttm110) REVERT: A 1094 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9164 (t) REVERT: B 153 MET cc_start: 0.3686 (OUTLIER) cc_final: 0.1936 (ptt) REVERT: B 544 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7538 (m110) REVERT: B 554 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7157 (tp30) REVERT: C 96 GLU cc_start: 0.5773 (OUTLIER) cc_final: 0.5121 (pm20) REVERT: C 153 MET cc_start: 0.2438 (mpp) cc_final: -0.0361 (ttm) REVERT: C 518 LEU cc_start: -0.0493 (OUTLIER) cc_final: -0.0957 (tp) REVERT: C 529 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7589 (tppt) REVERT: C 814 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7657 (mmtt) REVERT: H 34 MET cc_start: 0.4663 (mpm) cc_final: 0.4233 (mpm) REVERT: H 114 MET cc_start: -0.1621 (mtm) cc_final: -0.1958 (mtp) REVERT: H 178 HIS cc_start: 0.0759 (OUTLIER) cc_final: 0.0040 (m-70) REVERT: I 83 MET cc_start: 0.2711 (mmp) cc_final: 0.1633 (mtp) REVERT: I 106 ASP cc_start: 0.3967 (OUTLIER) cc_final: 0.3293 (m-30) REVERT: I 184 LEU cc_start: 0.2825 (OUTLIER) cc_final: 0.2294 (pt) REVERT: I 211 ASN cc_start: 0.1535 (OUTLIER) cc_final: 0.0297 (m110) REVERT: M 136 VAL cc_start: 0.1080 (OUTLIER) cc_final: 0.0808 (m) outliers start: 170 outliers final: 68 residues processed: 302 average time/residue: 0.4663 time to fit residues: 176.4159 Evaluate side-chains 217 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 131 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 750 SER 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 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 374 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 267 optimal weight: 4.9990 chunk 348 optimal weight: 50.0000 chunk 244 optimal weight: 0.2980 chunk 278 optimal weight: 3.9990 chunk 142 optimal weight: 0.0470 chunk 203 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.207935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.161071 restraints weight = 49748.445| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.62 r_work: 0.3090 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31650 Z= 0.126 Angle : 0.708 13.304 43232 Z= 0.335 Chirality : 0.048 0.604 5077 Planarity : 0.004 0.063 5461 Dihedral : 5.837 59.360 4145 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.48 % Favored : 92.34 % Rotamer: Outliers : 4.74 % Allowed : 22.56 % Favored : 72.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.13), residues: 3798 helix: 0.98 (0.20), residues: 701 sheet: -0.23 (0.15), residues: 1082 loop : -2.08 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.001 PHE C 106 TRP 0.010 0.001 TRP L 188 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (31533) covalent geometry : angle 0.67438 / 0.33 (42927) SS BOND : bond 0.00358 / 0.23 ( 46) SS BOND : angle 1.73354 / 1.13 ( 92) hydrogen bonds : bond 0.03820 / 2.53 ( 1096) hydrogen bonds : angle 5.18750 / 3.58 ( 3108) link_BETA1-4 : bond 0.00551 / 0.30 ( 23) link_BETA1-4 : angle 2.16257 / 1.37 ( 69) link_NAG-ASN : bond 0.00734 / 0.37 ( 48) link_NAG-ASN : angle 3.30003 / 2.05 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 140 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.6974 (p90) cc_final: 0.6690 (p90) REVERT: A 190 ARG cc_start: 0.8466 (mtt90) cc_final: 0.7900 (mmm-85) REVERT: A 333 THR cc_start: 0.5362 (OUTLIER) cc_final: 0.4950 (t) REVERT: A 335 LEU cc_start: 0.4863 (OUTLIER) cc_final: 0.4641 (mp) REVERT: A 379 CYS cc_start: 0.1974 (OUTLIER) cc_final: 0.1133 (p) REVERT: A 546 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.6955 (mm) REVERT: A 1019 ARG cc_start: 0.9008 (tpt170) cc_final: 0.8807 (ttm110) REVERT: A 1094 VAL cc_start: 0.9376 (OUTLIER) cc_final: 0.9104 (t) REVERT: B 122 ASN cc_start: 0.4934 (OUTLIER) cc_final: 0.4537 (m-40) REVERT: B 153 MET cc_start: 0.3717 (mpp) cc_final: 0.1953 (ptt) REVERT: B 554 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: C 96 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5402 (pm20) REVERT: C 153 MET cc_start: 0.1948 (mpp) cc_final: -0.0416 (ttm) REVERT: C 518 LEU cc_start: -0.0666 (OUTLIER) cc_final: -0.0967 (mt) REVERT: C 529 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7512 (tppt) REVERT: C 537 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8296 (mtmm) REVERT: C 814 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7708 (mmtt) REVERT: H 34 MET cc_start: 0.4718 (mpm) cc_final: 0.4401 (mpm) REVERT: H 114 MET cc_start: -0.1750 (mtm) cc_final: -0.2150 (mtp) REVERT: H 178 HIS cc_start: 0.0806 (OUTLIER) cc_final: 0.0178 (m-70) REVERT: L 152 LYS cc_start: 0.1608 (OUTLIER) cc_final: 0.1283 (ptpt) REVERT: I 34 MET cc_start: 0.3841 (OUTLIER) cc_final: 0.2727 (mpt) REVERT: I 83 MET cc_start: 0.2828 (mmp) cc_final: 0.1946 (mtp) REVERT: I 106 ASP cc_start: 0.4003 (OUTLIER) cc_final: 0.3391 (m-30) REVERT: I 114 MET cc_start: -0.0044 (OUTLIER) cc_final: -0.0434 (pp-130) REVERT: I 184 LEU cc_start: 0.2805 (OUTLIER) cc_final: 0.2265 (pt) REVERT: I 211 ASN cc_start: 0.1582 (OUTLIER) cc_final: 0.0328 (m110) REVERT: M 136 VAL cc_start: 0.1105 (OUTLIER) cc_final: 0.0813 (m) REVERT: M 183 LEU cc_start: -0.0192 (OUTLIER) cc_final: -0.1177 (tp) REVERT: M 195 SER cc_start: 0.2509 (OUTLIER) cc_final: 0.2042 (m) outliers start: 159 outliers final: 77 residues processed: 283 average time/residue: 0.4479 time to fit residues: 161.8518 Evaluate side-chains 226 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 127 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR 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 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 152 LYS Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 284 optimal weight: 0.9990 chunk 326 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 chunk 305 optimal weight: 40.0000 chunk 261 optimal weight: 6.9990 chunk 336 optimal weight: 20.0000 chunk 213 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 804 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 935 GLN ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN L 35 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** 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 = 0.4457 r_free = 0.4457 target = 0.205664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156079 restraints weight = 48806.205| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.62 r_work: 0.2990 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.115 31650 Z= 0.431 Angle : 0.947 14.819 43232 Z= 0.453 Chirality : 0.063 0.907 5077 Planarity : 0.006 0.064 5461 Dihedral : 6.427 59.384 4142 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.98 % Favored : 90.84 % Rotamer: Outliers : 5.60 % Allowed : 21.82 % Favored : 72.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -1.85 (0.13), residues: 3798 helix: 0.14 (0.19), residues: 708 sheet: -0.44 (0.15), residues: 1101 loop : -2.28 (0.12), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1039 TYR 0.024 0.003 TYR A1067 PHE 0.030 0.003 PHE A 86 TRP 0.019 0.003 TRP C 436 HIS 0.008 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01063 / 0.43 (31533) covalent geometry : angle 0.90998 / 0.44 (42927) SS BOND : bond 0.00731 / 0.47 ( 46) SS BOND : angle 2.37356 / 1.51 ( 92) hydrogen bonds : bond 0.06504 / 4.28 ( 1096) hydrogen bonds : angle 5.82311 / 4.03 ( 3108) link_BETA1-4 : bond 0.00676 / 0.40 ( 23) link_BETA1-4 : angle 2.73138 / 1.79 ( 69) link_NAG-ASN : bond 0.01139 / 0.71 ( 48) link_NAG-ASN : angle 3.91413 / 2.52 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 136 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.6907 (p90) cc_final: 0.6649 (p90) REVERT: A 333 THR cc_start: 0.4880 (OUTLIER) cc_final: 0.4572 (t) REVERT: A 379 CYS cc_start: 0.2071 (OUTLIER) cc_final: 0.1547 (p) REVERT: A 546 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7053 (mm) REVERT: A 869 MET cc_start: 0.9334 (mtt) cc_final: 0.9043 (mtt) REVERT: A 1094 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9169 (t) REVERT: A 1113 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8651 (mt0) REVERT: B 153 MET cc_start: 0.3834 (OUTLIER) cc_final: 0.1875 (ppp) REVERT: B 237 ARG cc_start: 0.7508 (mtm180) cc_final: 0.7243 (ttm-80) REVERT: B 537 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7767 (mttt) REVERT: B 554 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: B 702 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: C 153 MET cc_start: 0.1714 (mpp) cc_final: -0.0062 (ttt) REVERT: C 518 LEU cc_start: -0.0485 (OUTLIER) cc_final: -0.0695 (tp) REVERT: C 529 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7701 (tppt) REVERT: C 535 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7707 (ttmt) REVERT: C 1029 MET cc_start: 0.9404 (tpp) cc_final: 0.9137 (tpp) REVERT: H 34 MET cc_start: 0.4846 (mpm) cc_final: 0.4620 (mpm) REVERT: H 60 TYR cc_start: 0.2628 (OUTLIER) cc_final: 0.1982 (m-10) REVERT: H 114 MET cc_start: -0.1513 (mtm) cc_final: -0.2090 (mtp) REVERT: H 178 HIS cc_start: 0.0638 (OUTLIER) cc_final: 0.0022 (m-70) REVERT: I 34 MET cc_start: 0.4173 (OUTLIER) cc_final: 0.2976 (mpt) REVERT: I 83 MET cc_start: 0.2786 (mmp) cc_final: 0.2009 (mtp) REVERT: I 106 ASP cc_start: 0.4358 (OUTLIER) cc_final: 0.3650 (m-30) REVERT: I 211 ASN cc_start: 0.0878 (OUTLIER) cc_final: -0.0139 (m110) REVERT: M 134 THR cc_start: 0.0069 (m) cc_final: -0.0252 (t) REVERT: M 195 SER cc_start: 0.2369 (OUTLIER) cc_final: 0.1957 (m) outliers start: 188 outliers final: 103 residues processed: 299 average time/residue: 0.4333 time to fit residues: 165.6468 Evaluate side-chains 243 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 122 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE 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 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 99 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 366 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.208105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158455 restraints weight = 49241.136| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.69 r_work: 0.3030 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31650 Z= 0.152 Angle : 0.748 12.786 43232 Z= 0.352 Chirality : 0.050 0.683 5077 Planarity : 0.005 0.055 5461 Dihedral : 5.974 58.701 4141 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.90 % Favored : 92.89 % Rotamer: Outliers : 4.23 % Allowed : 23.52 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.13), residues: 3798 helix: 0.67 (0.20), residues: 704 sheet: -0.19 (0.15), residues: 1065 loop : -2.08 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.019 0.001 TYR B1067 PHE 0.028 0.001 PHE A 140 TRP 0.015 0.001 TRP L 151 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (31533) covalent geometry : angle 0.71796 / 0.34 (42927) SS BOND : bond 0.00526 / 0.30 ( 46) SS BOND : angle 1.73834 / 1.09 ( 92) hydrogen bonds : bond 0.04360 / 2.87 ( 1096) hydrogen bonds : angle 5.39898 / 3.73 ( 3108) link_BETA1-4 : bond 0.00550 / 0.30 ( 23) link_BETA1-4 : angle 2.02406 / 1.24 ( 69) link_NAG-ASN : bond 0.00864 / 0.44 ( 48) link_NAG-ASN : angle 3.24951 / 2.08 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 136 time to evaluate : 1.174 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 160 TYR cc_start: 0.6926 (p90) cc_final: 0.6618 (p90) REVERT: A 333 THR cc_start: 0.5187 (OUTLIER) cc_final: 0.4877 (t) REVERT: A 379 CYS cc_start: 0.1943 (OUTLIER) cc_final: 0.1415 (p) REVERT: A 546 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7109 (mm) REVERT: A 568 ASP cc_start: 0.8588 (p0) cc_final: 0.8369 (p0) REVERT: A 1094 VAL cc_start: 0.9384 (OUTLIER) cc_final: 0.9152 (t) REVERT: A 1113 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8743 (mt0) REVERT: B 153 MET cc_start: 0.3651 (OUTLIER) cc_final: 0.1852 (tmm) REVERT: B 554 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7164 (tp30) REVERT: C 96 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5506 (pm20) REVERT: C 153 MET cc_start: 0.1659 (mpp) cc_final: -0.0132 (ttt) REVERT: C 518 LEU cc_start: -0.0511 (OUTLIER) cc_final: -0.0742 (tp) REVERT: C 529 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7633 (tppt) REVERT: C 1029 MET cc_start: 0.9312 (tpp) cc_final: 0.9093 (tpp) REVERT: H 114 MET cc_start: -0.1584 (mtm) cc_final: -0.2057 (mtp) REVERT: H 178 HIS cc_start: 0.0594 (OUTLIER) cc_final: 0.0006 (m-70) REVERT: I 34 MET cc_start: 0.3969 (OUTLIER) cc_final: 0.2807 (mpt) REVERT: I 83 MET cc_start: 0.2452 (mmp) cc_final: 0.1653 (mtp) REVERT: I 106 ASP cc_start: 0.4260 (OUTLIER) cc_final: 0.3640 (m-30) REVERT: I 114 MET cc_start: -0.0743 (OUTLIER) cc_final: -0.1048 (pp-130) REVERT: I 211 ASN cc_start: 0.0721 (OUTLIER) cc_final: -0.0324 (m110) REVERT: M 134 THR cc_start: 0.0055 (m) cc_final: -0.0263 (t) REVERT: M 195 SER cc_start: 0.2415 (OUTLIER) cc_final: 0.2161 (m) outliers start: 142 outliers final: 85 residues processed: 261 average time/residue: 0.4133 time to fit residues: 138.3891 Evaluate side-chains 223 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 122 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL 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 315 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL 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 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 343 optimal weight: 40.0000 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 277 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 309 optimal weight: 50.0000 chunk 101 optimal weight: 8.9990 chunk 170 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 ASN ** L 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 ASN ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.207384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.158428 restraints weight = 49417.543| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.62 r_work: 0.3052 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31650 Z= 0.139 Angle : 0.712 14.089 43232 Z= 0.335 Chirality : 0.049 0.727 5077 Planarity : 0.005 0.053 5461 Dihedral : 5.673 59.888 4141 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.64 % Favored : 92.21 % Rotamer: Outliers : 3.93 % Allowed : 23.79 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.21 (0.13), residues: 3798 helix: 0.98 (0.20), residues: 702 sheet: -0.11 (0.15), residues: 1068 loop : -1.92 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.019 0.001 TYR B1067 PHE 0.018 0.001 PHE C 106 TRP 0.010 0.001 TRP L 188 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (31533) covalent geometry : angle 0.68220 / 0.33 (42927) SS BOND : bond 0.00405 / 0.25 ( 46) SS BOND : angle 1.63871 / 0.99 ( 92) hydrogen bonds : bond 0.03996 / 2.64 ( 1096) hydrogen bonds : angle 5.20797 / 3.60 ( 3108) link_BETA1-4 : bond 0.00491 / 0.26 ( 23) link_BETA1-4 : angle 1.80918 / 1.12 ( 69) link_NAG-ASN : bond 0.01022 / 0.47 ( 48) link_NAG-ASN : angle 3.19698 / 2.01 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 141 time to evaluate : 1.022 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 160 TYR cc_start: 0.6948 (p90) cc_final: 0.6611 (p90) REVERT: A 333 THR cc_start: 0.4913 (OUTLIER) cc_final: 0.4576 (t) REVERT: A 379 CYS cc_start: 0.1905 (OUTLIER) cc_final: 0.1326 (p) REVERT: A 546 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7088 (mm) REVERT: A 568 ASP cc_start: 0.8580 (p0) cc_final: 0.8352 (p0) REVERT: A 855 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.5992 (t80) REVERT: A 1094 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9119 (t) REVERT: A 1113 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8810 (mt0) REVERT: B 153 MET cc_start: 0.3601 (OUTLIER) cc_final: 0.1835 (tmm) REVERT: B 233 ILE cc_start: 0.6337 (OUTLIER) cc_final: 0.5818 (tp) REVERT: B 237 ARG cc_start: 0.7466 (mtm180) cc_final: 0.7236 (ttm-80) REVERT: B 281 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: B 554 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7178 (tp30) REVERT: C 153 MET cc_start: 0.1650 (mpp) cc_final: -0.0236 (ttt) REVERT: C 518 LEU cc_start: -0.0438 (OUTLIER) cc_final: -0.0684 (mt) REVERT: C 529 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7536 (tppt) REVERT: H 114 MET cc_start: -0.2004 (mtm) cc_final: -0.2478 (mtp) REVERT: H 178 HIS cc_start: 0.0610 (OUTLIER) cc_final: 0.0014 (m-70) REVERT: I 34 MET cc_start: 0.3904 (OUTLIER) cc_final: 0.2784 (mpt) REVERT: I 50 VAL cc_start: 0.5034 (t) cc_final: 0.4786 (m) REVERT: I 60 TYR cc_start: 0.2366 (OUTLIER) cc_final: 0.1810 (m-10) REVERT: I 83 MET cc_start: 0.2624 (mmp) cc_final: 0.1825 (mtp) REVERT: I 114 MET cc_start: -0.0972 (OUTLIER) cc_final: -0.1250 (pp-130) REVERT: I 211 ASN cc_start: 0.0736 (OUTLIER) cc_final: -0.0286 (m110) REVERT: M 134 THR cc_start: -0.0379 (m) cc_final: -0.0771 (t) outliers start: 132 outliers final: 86 residues processed: 252 average time/residue: 0.3828 time to fit residues: 125.7416 Evaluate side-chains 223 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 120 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL 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 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 381 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 239 optimal weight: 0.0870 chunk 288 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 303 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 269 optimal weight: 0.5980 chunk 214 optimal weight: 30.0000 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.205685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.156970 restraints weight = 49201.963| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.69 r_work: 0.3065 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31650 Z= 0.139 Angle : 0.716 22.044 43232 Z= 0.334 Chirality : 0.049 0.606 5077 Planarity : 0.004 0.054 5461 Dihedral : 5.557 59.809 4141 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.29 % Favored : 92.55 % Rotamer: Outliers : 3.61 % Allowed : 24.14 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.09 (0.13), residues: 3798 helix: 1.10 (0.20), residues: 702 sheet: -0.02 (0.15), residues: 1066 loop : -1.85 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.019 0.001 TYR B1067 PHE 0.028 0.001 PHE A 140 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (31533) covalent geometry : angle 0.67967 / 0.33 (42927) SS BOND : bond 0.00403 / 0.26 ( 46) SS BOND : angle 1.61814 / 0.98 ( 92) hydrogen bonds : bond 0.03980 / 2.63 ( 1096) hydrogen bonds : angle 5.15921 / 3.57 ( 3108) link_BETA1-4 : bond 0.00500 / 0.26 ( 23) link_BETA1-4 : angle 1.77241 / 1.09 ( 69) link_NAG-ASN : bond 0.00613 / 0.34 ( 48) link_NAG-ASN : angle 3.61893 / 2.20 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 130 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.6788 (p90) cc_final: 0.6481 (p90) REVERT: A 333 THR cc_start: 0.4683 (OUTLIER) cc_final: 0.4358 (t) REVERT: A 379 CYS cc_start: 0.1843 (OUTLIER) cc_final: 0.1181 (p) REVERT: A 546 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7042 (mm) REVERT: A 568 ASP cc_start: 0.8535 (p0) cc_final: 0.8332 (p0) REVERT: A 855 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.5860 (t80) REVERT: A 1113 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8766 (mt0) REVERT: B 153 MET cc_start: 0.3596 (OUTLIER) cc_final: 0.1865 (tmm) REVERT: B 233 ILE cc_start: 0.6172 (OUTLIER) cc_final: 0.5687 (tp) REVERT: B 554 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7338 (tp30) REVERT: C 153 MET cc_start: 0.1241 (mpp) cc_final: -0.0498 (ttt) REVERT: C 518 LEU cc_start: -0.0255 (OUTLIER) cc_final: -0.0549 (mt) REVERT: C 529 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7654 (tppt) REVERT: H 34 MET cc_start: 0.4707 (mpm) cc_final: 0.4450 (mpm) REVERT: H 114 MET cc_start: -0.2118 (mtm) cc_final: -0.2505 (mtp) REVERT: H 178 HIS cc_start: 0.0713 (OUTLIER) cc_final: 0.0038 (m-70) REVERT: H 184 LEU cc_start: 0.1387 (OUTLIER) cc_final: 0.1084 (tt) REVERT: I 34 MET cc_start: 0.4040 (OUTLIER) cc_final: 0.2748 (mpt) REVERT: I 50 VAL cc_start: 0.5157 (t) cc_final: 0.4905 (m) REVERT: I 60 TYR cc_start: 0.2430 (OUTLIER) cc_final: 0.1840 (m-10) REVERT: I 83 MET cc_start: 0.2666 (mmp) cc_final: 0.1977 (mtp) REVERT: I 114 MET cc_start: -0.0462 (OUTLIER) cc_final: -0.0743 (pp-130) REVERT: I 211 ASN cc_start: 0.0733 (OUTLIER) cc_final: -0.0385 (m110) REVERT: M 134 THR cc_start: -0.0324 (m) cc_final: -0.0735 (t) outliers start: 121 outliers final: 85 residues processed: 234 average time/residue: 0.3689 time to fit residues: 112.5786 Evaluate side-chains 224 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 123 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL 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 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 182 optimal weight: 4.9990 chunk 379 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 234 optimal weight: 0.9980 chunk 377 optimal weight: 2.9990 chunk 209 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 230 optimal weight: 0.0970 chunk 279 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 369 optimal weight: 50.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.205646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.156587 restraints weight = 48927.594| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 3.54 r_work: 0.3065 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31650 Z= 0.141 Angle : 0.705 13.791 43232 Z= 0.331 Chirality : 0.049 0.600 5077 Planarity : 0.005 0.053 5461 Dihedral : 5.503 59.923 4141 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.50 % Favored : 92.34 % Rotamer: Outliers : 3.43 % Allowed : 24.38 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3798 helix: 1.16 (0.20), residues: 702 sheet: 0.04 (0.15), residues: 1065 loop : -1.82 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 237 TYR 0.019 0.001 TYR B1067 PHE 0.019 0.001 PHE C 106 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (31533) covalent geometry : angle 0.67686 / 0.32 (42927) SS BOND : bond 0.00403 / 0.26 ( 46) SS BOND : angle 1.58204 / 0.96 ( 92) hydrogen bonds : bond 0.03993 / 2.64 ( 1096) hydrogen bonds : angle 5.12926 / 3.55 ( 3108) link_BETA1-4 : bond 0.00510 / 0.27 ( 23) link_BETA1-4 : angle 1.75301 / 1.08 ( 69) link_NAG-ASN : bond 0.00623 / 0.34 ( 48) link_NAG-ASN : angle 3.11000 / 1.94 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 128 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.6750 (p90) cc_final: 0.6504 (p90) REVERT: A 303 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7738 (mp) REVERT: A 333 THR cc_start: 0.4715 (OUTLIER) cc_final: 0.4441 (t) REVERT: A 379 CYS cc_start: 0.1828 (OUTLIER) cc_final: 0.1180 (p) REVERT: A 546 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7036 (mm) REVERT: A 1113 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8767 (mt0) REVERT: B 153 MET cc_start: 0.3786 (OUTLIER) cc_final: 0.1951 (tmm) REVERT: B 233 ILE cc_start: 0.6307 (OUTLIER) cc_final: 0.5850 (tp) REVERT: B 237 ARG cc_start: 0.7512 (mtm180) cc_final: 0.7167 (ttm-80) REVERT: B 281 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8262 (pp20) REVERT: B 554 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: C 153 MET cc_start: 0.1308 (mpp) cc_final: -0.0420 (ttt) REVERT: C 529 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7605 (tppt) REVERT: H 34 MET cc_start: 0.4864 (mpm) cc_final: 0.4567 (mpm) REVERT: H 114 MET cc_start: -0.2209 (mtm) cc_final: -0.2566 (mtp) REVERT: H 178 HIS cc_start: 0.0667 (OUTLIER) cc_final: 0.0032 (m-70) REVERT: H 184 LEU cc_start: 0.1280 (OUTLIER) cc_final: 0.1012 (tt) REVERT: I 34 MET cc_start: 0.4032 (OUTLIER) cc_final: 0.2873 (mpt) REVERT: I 50 VAL cc_start: 0.5196 (t) cc_final: 0.4942 (m) REVERT: I 60 TYR cc_start: 0.2538 (OUTLIER) cc_final: 0.1914 (m-10) REVERT: I 83 MET cc_start: 0.2293 (mmp) cc_final: 0.1671 (mtp) REVERT: I 114 MET cc_start: -0.0793 (OUTLIER) cc_final: -0.1006 (pp-130) REVERT: I 211 ASN cc_start: 0.0739 (OUTLIER) cc_final: -0.0223 (m110) REVERT: M 134 THR cc_start: -0.0332 (m) cc_final: -0.0736 (t) REVERT: M 152 LYS cc_start: 0.1406 (OUTLIER) cc_final: 0.0745 (mppt) outliers start: 115 outliers final: 86 residues processed: 227 average time/residue: 0.3900 time to fit residues: 114.8778 Evaluate side-chains 225 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 122 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL 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 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 152 LYS Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 277 optimal weight: 0.9990 chunk 342 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 355 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 325 optimal weight: 30.0000 chunk 185 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.205611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.156782 restraints weight = 49159.619| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.60 r_work: 0.3031 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31650 Z= 0.208 Angle : 0.755 12.527 43232 Z= 0.358 Chirality : 0.051 0.707 5077 Planarity : 0.005 0.054 5461 Dihedral : 5.685 57.752 4141 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.06 % Favored : 91.79 % Rotamer: Outliers : 3.58 % Allowed : 24.26 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 3798 helix: 0.88 (0.20), residues: 707 sheet: 0.06 (0.15), residues: 1065 loop : -1.87 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 190 TYR 0.021 0.001 TYR B1067 PHE 0.028 0.002 PHE A 140 TRP 0.015 0.002 TRP C 436 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (31533) covalent geometry : angle 0.72687 / 0.35 (42927) SS BOND : bond 0.00476 / 0.31 ( 46) SS BOND : angle 1.85065 / 1.13 ( 92) hydrogen bonds : bond 0.04824 / 3.18 ( 1096) hydrogen bonds : angle 5.34831 / 3.71 ( 3108) link_BETA1-4 : bond 0.00517 / 0.28 ( 23) link_BETA1-4 : angle 1.89156 / 1.17 ( 69) link_NAG-ASN : bond 0.00688 / 0.36 ( 48) link_NAG-ASN : angle 3.11939 / 1.99 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10004.72 seconds wall clock time: 171 minutes 25.98 seconds (10285.98 seconds total)