Starting phenix.real_space_refine on Mon Sep 14 14:11:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7czt_30516/09_2026/7czt_30516.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czt_30516/09_2026/7czt_30516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7czt_30516/09_2026/7czt_30516.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7czt_30516/09_2026/7czt_30516.cif" model { file = "/net/cci-nas-00/data/ceres_data/7czt_30516/09_2026/7czt_30516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czt_30516/09_2026/7czt_30516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7czt_30516/09_2026/7czt_30516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czt_30516/09_2026/7czt_30516.map" } resolution = 2.7 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= 0.005 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 129 5.16 5 C 19735 2.51 5 N 5070 2.21 5 O 6126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31060 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1677 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain: "L" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1657 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 19, 'TRANS': 199} Chain: "I" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1677 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain: "M" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1657 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 19, 'TRANS': 199} 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: "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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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: 6.67, per 1000 atoms: 0.21 Number of scatterers: 31060 At special positions: 0 Unit cell: (134.788, 176.094, 238.053, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 6126 8.00 N 5070 7.00 C 19735 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.64 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.58 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 144 " - pdb=" SG CYS L 203 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 146 " - pdb=" SG CYS I 202 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 144 " - pdb=" SG CYS M 203 " 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 B1410 " - " NAG B1411 " " 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-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 343 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 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 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7232 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 68 sheets defined 19.7% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.771A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.652A 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: 4.177A 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: 3.539A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A 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 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.640A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 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: 3.544A 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: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.582A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.604A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.594A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 131 through 137 Processing helix chain 'L' and resid 191 through 198 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.595A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 131 through 137 Processing helix chain 'M' and resid 191 through 198 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: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A 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: 4.438A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A 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: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A 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) removed outlier: 6.949A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A 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: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A 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: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.538A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.649A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A 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=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.757A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS C 291 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.667A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.863A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.231A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A 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: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, 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: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A 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=AE7, 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=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.619A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.375A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY H 33 " --> pdb=" O TRP H 99 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.375A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.008A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.008A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 156 through 160 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.856A pdb=" N THR L 114 " --> pdb=" O SER L 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA L 92 " --> pdb=" O VAL L 113 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE L 35 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR L 51 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.856A pdb=" N THR L 114 " --> pdb=" O SER L 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA L 92 " --> pdb=" O VAL L 113 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.512A pdb=" N THR L 78 " --> pdb=" O ASP L 73 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 124 through 128 Processing sheet with id=AG1, first strand: chain 'L' and resid 124 through 128 Processing sheet with id=AG2, first strand: chain 'L' and resid 164 through 165 removed outlier: 4.441A pdb=" N TRP L 158 " --> pdb=" O VAL L 165 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 5 through 7 removed outlier: 3.619A pdb=" N SER I 71 " --> pdb=" O TYR I 80 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.375A pdb=" N GLY I 10 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY I 33 " --> pdb=" O TRP I 99 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.375A pdb=" N GLY I 10 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 126 through 130 removed outlier: 5.009A pdb=" N ALA I 143 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 190 " --> pdb=" O ALA I 143 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY I 145 " --> pdb=" O VAL I 188 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL I 188 " --> pdb=" O GLY I 145 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 147 " --> pdb=" O SER I 186 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER I 186 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 149 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 184 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 126 through 130 removed outlier: 5.009A pdb=" N ALA I 143 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 190 " --> pdb=" O ALA I 143 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY I 145 " --> pdb=" O VAL I 188 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL I 188 " --> pdb=" O GLY I 145 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 147 " --> pdb=" O SER I 186 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER I 186 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 149 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 184 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 156 through 160 Processing sheet with id=AG9, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.856A pdb=" N THR M 114 " --> pdb=" O SER M 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA M 92 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE M 35 " --> pdb=" O TYR M 51 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR M 51 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.856A pdb=" N THR M 114 " --> pdb=" O SER M 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA M 92 " --> pdb=" O VAL M 113 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 17 through 23 removed outlier: 3.512A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 124 through 128 Processing sheet with id=AH4, first strand: chain 'M' and resid 124 through 128 Processing sheet with id=AH5, first strand: chain 'M' and resid 164 through 165 removed outlier: 4.441A pdb=" N TRP M 158 " --> pdb=" O VAL M 165 " (cutoff:3.500A) 1215 hydrogen bonds defined for protein. 3261 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: 7.89 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9670 1.34 - 1.46: 8245 1.46 - 1.59: 13686 1.59 - 1.72: 0 1.72 - 1.84: 162 Bond restraints: 31763 Sorted by residual: bond pdb=" C THR C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.34e-02 5.57e+03 1.82e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.067 1.59e-02 3.96e+03 1.77e+01 bond pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" C LEU A 223 " pdb=" N GLU A 224 " ideal model delta sigma weight residual 1.331 1.391 -0.060 2.07e-02 2.33e+03 8.36e+00 bond pdb=" C ILE A 664 " pdb=" N PRO A 665 " ideal model delta sigma weight residual 1.335 1.311 0.024 8.70e-03 1.32e+04 7.46e+00 ... (remaining 31758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 42250 2.70 - 5.40: 903 5.40 - 8.10: 72 8.10 - 10.80: 5 10.80 - 13.50: 2 Bond angle restraints: 43232 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.84 -11.30 1.91e+00 2.74e-01 3.50e+01 angle pdb=" N GLU C 156 " pdb=" CA GLU C 156 " pdb=" C GLU C 156 " ideal model delta sigma weight residual 108.45 115.82 -7.37 1.26e+00 6.30e-01 3.42e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 119.78 114.03 5.75 1.03e+00 9.43e-01 3.12e+01 angle pdb=" C LEU B 212 " pdb=" N VAL B 213 " pdb=" CA VAL B 213 " ideal model delta sigma weight residual 123.08 117.65 5.43 1.01e+00 9.80e-01 2.89e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 122.56 115.24 7.32 1.50e+00 4.44e-01 2.38e+01 ... (remaining 43227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 15723 17.92 - 35.83: 1920 35.83 - 53.75: 515 53.75 - 71.66: 137 71.66 - 89.58: 53 Dihedral angle restraints: 18348 sinusoidal: 7095 harmonic: 11253 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.14 80.86 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.60 73.40 1 1.00e+01 1.00e-02 6.86e+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 21.08 71.92 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 18345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5090 0.328 - 0.657: 3 0.657 - 0.985: 2 0.985 - 1.313: 1 1.313 - 1.642: 1 Chirality restraints: 5097 Sorted by residual: chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " 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 b 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.74e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.19 -1.21 2.00e-01 2.50e+01 3.66e+01 ... (remaining 5094 not shown) Planarity restraints: 5528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.049 2.00e-02 2.50e+03 8.12e-02 8.25e+01 pdb=" CG ASN C 331 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.145 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " -0.022 2.00e-02 2.50e+03 3.15e-02 1.24e+01 pdb=" CG ASN C1134 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " 0.056 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU L 24 " -0.051 5.00e-02 4.00e+02 7.85e-02 9.85e+00 pdb=" N PRO L 25 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO L 25 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 25 " -0.042 5.00e-02 4.00e+02 ... (remaining 5525 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 342 2.57 - 3.15: 24578 3.15 - 3.73: 44931 3.73 - 4.32: 66247 4.32 - 4.90: 110823 Nonbonded interactions: 246921 Sorted by model distance: nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.981 3.120 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 3.120 nonbonded pdb=" O ALA A 522 " pdb=" OG1 THR A 523 " model vdw 2.137 3.040 nonbonded pdb=" O ALA C 522 " pdb=" OG1 THR C 523 " model vdw 2.138 3.040 nonbonded pdb=" O SER A 813 " pdb=" OG SER A 813 " model vdw 2.183 3.040 ... (remaining 246916 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 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 620 or resid 641 through 939 or resid 944 through 14 \ 08)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1408)) selection = (chain 'C' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 826 or resid 855 through 1408)) } 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' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 29.100 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.012 0.610 31879 Z= 0.538 Angle : 1.171 48.925 43534 Z= 0.615 Chirality : 0.069 1.642 5097 Planarity : 0.006 0.078 5480 Dihedral : 17.803 89.576 10978 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.88 % Favored : 89.14 % Rotamer: Outliers : 11.97 % Allowed : 20.84 % Favored : 67.19 % 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: -3.68 (0.11), residues: 3804 helix: -2.14 (0.16), residues: 679 sheet: -1.67 (0.14), residues: 1145 loop : -3.09 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.027 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.003 TRP A 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01104 / 0.48 (31763) covalent geometry : angle 0.98209 / 0.56 (43232) SS BOND : bond 0.12360 / 6.22 ( 46) SS BOND : angle 9.26985 / 5.60 ( 92) hydrogen bonds : bond 0.17352 / 11.52 ( 1119) hydrogen bonds : angle 7.61247 / 5.19 ( 3261) link_BETA1-4 : bond 0.04170 / 3.21 ( 22) link_BETA1-4 : angle 4.32506 / 2.63 ( 66) link_NAG-ASN : bond 0.01913 / 0.79 ( 48) link_NAG-ASN : angle 7.82119 / 5.54 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 403 poor density : 270 time to evaluate : 1.210 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 66 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.6533 (t-90) REVERT: A 153 MET cc_start: 0.1034 (mpp) cc_final: -0.1601 (ptt) REVERT: A 158 ARG cc_start: 0.5441 (OUTLIER) cc_final: 0.4951 (mtp-110) REVERT: A 389 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.6300 (m-30) REVERT: A 394 ASN cc_start: 0.5333 (m-40) cc_final: 0.4879 (m-40) REVERT: A 588 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8492 (p) REVERT: A 692 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8713 (mt) REVERT: A 960 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8058 (m110) REVERT: A 1039 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8480 (mtp180) REVERT: A 1142 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7176 (mp10) REVERT: B 278 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8554 (ttmm) REVERT: B 472 ILE cc_start: 0.4451 (OUTLIER) cc_final: 0.4155 (pt) REVERT: B 473 TYR cc_start: 0.4558 (OUTLIER) cc_final: 0.2670 (m-80) REVERT: B 533 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7626 (pp) REVERT: C 54 LEU cc_start: 0.8892 (mm) cc_final: 0.8664 (mt) REVERT: C 86 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.5925 (t80) REVERT: C 88 ASP cc_start: 0.6265 (m-30) cc_final: 0.5790 (t0) REVERT: C 530 SER cc_start: 0.7544 (OUTLIER) cc_final: 0.7183 (m) REVERT: C 985 ASP cc_start: 0.6904 (p0) cc_final: 0.6535 (p0) REVERT: H 31 SER cc_start: 0.4899 (OUTLIER) cc_final: 0.4659 (p) REVERT: H 123 LYS cc_start: 0.3185 (OUTLIER) cc_final: 0.2658 (mtmt) REVERT: L 78 THR cc_start: 0.3741 (OUTLIER) cc_final: 0.3239 (m) REVERT: L 188 LEU cc_start: 0.1406 (tp) cc_final: 0.0961 (mt) REVERT: I 13 GLN cc_start: 0.2493 (OUTLIER) cc_final: 0.2007 (tm130) REVERT: I 123 LYS cc_start: 0.2905 (OUTLIER) cc_final: 0.2471 (mtmm) REVERT: M 93 ASP cc_start: 0.0104 (OUTLIER) cc_final: -0.0462 (m-30) REVERT: M 182 TYR cc_start: 0.2987 (m-80) cc_final: 0.2525 (m-80) outliers start: 403 outliers final: 184 residues processed: 642 average time/residue: 0.4104 time to fit residues: 338.2883 Evaluate side-chains 379 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 175 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER 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 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 746 SER 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 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 123 LYS Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 163 SER Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 123 LYS Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 137 ASN A 188 ASN A 239 GLN A 422 ASN A 440 ASN A 493 GLN A 498 GLN A 644 GLN A 690 GLN A 703 ASN A 755 GLN A 762 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 992 GLN A1002 GLN A1058 HIS B 115 GLN B 188 ASN B 422 ASN B 487 ASN B 540 ASN B 563 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 804 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1054 GLN C 66 HIS C 134 GLN C 188 ASN C 207 HIS C 321 GLN C 422 ASN C 440 ASN C 493 GLN C 498 GLN C 606 ASN C 641 ASN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1002 GLN C1010 GLN C1071 GLN C1101 HIS H 111 GLN L 40 GLN L 60 GLN L 102 ASN L 118 GLN L 138 ASN L 198 HIS L 204 GLN ** L 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN M 40 GLN M 102 ASN M 118 GLN M 198 HIS ** M 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.207820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.166064 restraints weight = 41685.304| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.33 r_work: 0.3339 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31879 Z= 0.157 Angle : 0.783 14.428 43534 Z= 0.387 Chirality : 0.050 0.500 5097 Planarity : 0.005 0.050 5480 Dihedral : 9.702 89.694 4441 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.47 % Favored : 92.40 % Rotamer: Outliers : 6.53 % Allowed : 23.25 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.28 (0.12), residues: 3804 helix: -0.14 (0.20), residues: 673 sheet: -0.72 (0.15), residues: 1100 loop : -2.54 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 995 TYR 0.020 0.002 TYR B1067 PHE 0.023 0.002 PHE A 140 TRP 0.013 0.001 TRP L 195 HIS 0.007 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (31763) covalent geometry : angle 0.74807 / 0.38 (43232) SS BOND : bond 0.00503 / 0.27 ( 46) SS BOND : angle 1.94055 / 1.25 ( 92) hydrogen bonds : bond 0.04915 / 3.26 ( 1119) hydrogen bonds : angle 5.86149 / 4.01 ( 3261) link_BETA1-4 : bond 0.00603 / 0.35 ( 22) link_BETA1-4 : angle 2.32306 / 1.44 ( 66) link_NAG-ASN : bond 0.00463 / 0.29 ( 48) link_NAG-ASN : angle 3.53212 / 2.20 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 213 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0522 (mpp) cc_final: -0.1848 (tmm) REVERT: A 347 PHE cc_start: 0.6364 (OUTLIER) cc_final: 0.6140 (t80) REVERT: A 389 ASP cc_start: 0.6248 (OUTLIER) cc_final: 0.5783 (m-30) REVERT: A 394 ASN cc_start: 0.5084 (m-40) cc_final: 0.4588 (m-40) REVERT: A 544 ASN cc_start: 0.8401 (p0) cc_final: 0.8187 (p0) REVERT: A 588 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8635 (p) REVERT: A 994 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: A 1142 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: B 355 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6160 (ttp-170) REVERT: B 406 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6309 (mm-30) REVERT: B 560 LEU cc_start: 0.5340 (OUTLIER) cc_final: 0.5023 (mp) REVERT: B 619 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: B 787 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8344 (mt0) REVERT: B 878 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8990 (tt) REVERT: B 912 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8784 (m) REVERT: C 88 ASP cc_start: 0.6623 (m-30) cc_final: 0.6202 (t0) REVERT: C 558 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8018 (mttm) REVERT: C 675 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7735 (tp40) REVERT: C 985 ASP cc_start: 0.7383 (p0) cc_final: 0.6979 (p0) REVERT: H 199 THR cc_start: 0.0217 (OUTLIER) cc_final: -0.0332 (m) REVERT: L 97 MET cc_start: 0.2831 (ttp) cc_final: 0.2574 (mtp) REVERT: I 123 LYS cc_start: 0.3143 (OUTLIER) cc_final: 0.2752 (mtmm) REVERT: I 176 LEU cc_start: 0.1268 (OUTLIER) cc_final: 0.0159 (pp) REVERT: M 196 LYS cc_start: 0.0386 (tptt) cc_final: 0.0040 (mmmt) REVERT: M 214 LYS cc_start: 0.2678 (mmtt) cc_final: 0.1749 (pmtt) outliers start: 220 outliers final: 93 residues processed: 410 average time/residue: 0.4497 time to fit residues: 232.3106 Evaluate side-chains 283 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 174 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS 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 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 123 LYS Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain I residue 123 LYS Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 163 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 307 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 267 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 202 optimal weight: 0.9980 chunk 350 optimal weight: 30.0000 chunk 129 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 291 optimal weight: 0.0980 chunk 383 optimal weight: 30.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 804 GLN A 856 ASN A1002 GLN A1011 GLN B 280 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 493 GLN C1002 GLN ** L 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.207380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.165785 restraints weight = 41587.375| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.24 r_work: 0.3311 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31879 Z= 0.166 Angle : 0.746 13.770 43534 Z= 0.366 Chirality : 0.049 0.498 5097 Planarity : 0.005 0.055 5480 Dihedral : 8.086 88.850 4247 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.75 % Favored : 92.19 % Rotamer: Outliers : 6.00 % Allowed : 23.31 % Favored : 70.69 % 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: -1.79 (0.13), residues: 3804 helix: 0.44 (0.20), residues: 678 sheet: -0.47 (0.15), residues: 1128 loop : -2.28 (0.12), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.022 0.002 TYR C1067 PHE 0.016 0.002 PHE B 515 TRP 0.012 0.001 TRP L 99 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (31763) covalent geometry : angle 0.71418 / 0.36 (43232) SS BOND : bond 0.00460 / 0.27 ( 46) SS BOND : angle 1.79772 / 1.16 ( 92) hydrogen bonds : bond 0.05052 / 3.34 ( 1119) hydrogen bonds : angle 5.57623 / 3.81 ( 3261) link_BETA1-4 : bond 0.00528 / 0.28 ( 22) link_BETA1-4 : angle 2.32716 / 1.44 ( 66) link_NAG-ASN : bond 0.00474 / 0.27 ( 48) link_NAG-ASN : angle 3.26588 / 2.06 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 201 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0644 (mpp) cc_final: -0.1703 (tmm) REVERT: A 158 ARG cc_start: 0.5385 (OUTLIER) cc_final: 0.4706 (mtp-110) REVERT: A 195 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8018 (mtmt) REVERT: A 347 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6261 (t80) REVERT: A 389 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5865 (m-30) REVERT: A 394 ASN cc_start: 0.4989 (m-40) cc_final: 0.4474 (m-40) REVERT: A 554 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: A 588 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8663 (p) REVERT: A 787 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7851 (mm110) REVERT: A 907 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8855 (m110) REVERT: A 994 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: A 1142 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: B 153 MET cc_start: 0.3067 (OUTLIER) cc_final: 0.1957 (tmt) REVERT: B 355 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6174 (ttp-170) REVERT: B 473 TYR cc_start: 0.4488 (OUTLIER) cc_final: 0.3757 (m-80) REVERT: B 614 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7962 (t0) REVERT: B 787 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: B 912 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8848 (m) REVERT: C 28 TYR cc_start: 0.7329 (m-80) cc_final: 0.6873 (m-80) REVERT: C 88 ASP cc_start: 0.6727 (m-30) cc_final: 0.6332 (t0) REVERT: C 314 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8316 (tp40) REVERT: C 558 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8024 (mmmt) REVERT: C 675 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7692 (tp40) REVERT: C 778 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8957 (m) REVERT: C 787 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8090 (mm-40) REVERT: C 985 ASP cc_start: 0.7269 (p0) cc_final: 0.6888 (p0) REVERT: H 34 MET cc_start: 0.3410 (mmm) cc_final: 0.2142 (mmt) REVERT: I 123 LYS cc_start: 0.2974 (OUTLIER) cc_final: 0.2543 (mtmm) REVERT: I 176 LEU cc_start: 0.1338 (OUTLIER) cc_final: 0.0126 (pp) REVERT: I 207 LYS cc_start: 0.2793 (OUTLIER) cc_final: 0.1820 (pttt) REVERT: M 181 LYS cc_start: 0.2821 (OUTLIER) cc_final: 0.2502 (ptpt) REVERT: M 182 TYR cc_start: 0.3187 (m-80) cc_final: 0.2866 (m-80) REVERT: M 196 LYS cc_start: 0.0693 (tptt) cc_final: 0.0360 (mmmt) outliers start: 202 outliers final: 114 residues processed: 377 average time/residue: 0.4724 time to fit residues: 224.0033 Evaluate side-chains 320 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 182 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 123 LYS Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 44 SER Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 163 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 206 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 14 optimal weight: 8.9990 chunk 240 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 chunk 351 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 309 optimal weight: 20.0000 chunk 364 optimal weight: 30.0000 chunk 229 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 856 ASN A 955 ASN A1002 GLN A1142 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 914 ASN C 675 GLN C1002 GLN ** L 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 GLN ** M 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.205657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.164335 restraints weight = 41120.653| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.26 r_work: 0.3392 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 31879 Z= 0.254 Angle : 0.816 15.804 43534 Z= 0.400 Chirality : 0.053 0.521 5097 Planarity : 0.005 0.057 5480 Dihedral : 8.118 87.060 4236 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.31 % Favored : 91.64 % Rotamer: Outliers : 6.98 % Allowed : 22.71 % Favored : 70.31 % 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: -1.71 (0.13), residues: 3804 helix: 0.37 (0.20), residues: 676 sheet: -0.23 (0.15), residues: 1114 loop : -2.29 (0.12), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 237 TYR 0.024 0.002 TYR B1067 PHE 0.021 0.002 PHE A 898 TRP 0.018 0.002 TRP A 104 HIS 0.029 0.002 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.25 (31763) covalent geometry : angle 0.78250 / 0.39 (43232) SS BOND : bond 0.00556 / 0.32 ( 46) SS BOND : angle 1.92729 / 1.25 ( 92) hydrogen bonds : bond 0.05921 / 3.92 ( 1119) hydrogen bonds : angle 5.68311 / 3.88 ( 3261) link_BETA1-4 : bond 0.00561 / 0.29 ( 22) link_BETA1-4 : angle 2.55030 / 1.59 ( 66) link_NAG-ASN : bond 0.00530 / 0.29 ( 48) link_NAG-ASN : angle 3.48616 / 2.21 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 193 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1199 (mpp) cc_final: -0.1453 (tmm) REVERT: A 158 ARG cc_start: 0.5607 (OUTLIER) cc_final: 0.4792 (mtp-110) REVERT: A 389 ASP cc_start: 0.6044 (OUTLIER) cc_final: 0.5601 (m-30) REVERT: A 394 ASN cc_start: 0.5079 (m-40) cc_final: 0.4701 (m-40) REVERT: A 554 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 787 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7928 (mm110) REVERT: A 907 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8714 (m110) REVERT: A 983 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7742 (ptt90) REVERT: A 985 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6606 (p0) REVERT: A 994 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: A 1142 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7388 (mp-120) REVERT: B 110 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5947 (tp) REVERT: B 153 MET cc_start: 0.2993 (OUTLIER) cc_final: 0.1760 (tmt) REVERT: B 224 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: B 355 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6188 (ttp-170) REVERT: B 473 TYR cc_start: 0.4677 (OUTLIER) cc_final: 0.4010 (m-80) REVERT: B 560 LEU cc_start: 0.5430 (OUTLIER) cc_final: 0.5129 (mp) REVERT: B 787 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8327 (mt0) REVERT: C 28 TYR cc_start: 0.7374 (m-80) cc_final: 0.6987 (m-80) REVERT: C 88 ASP cc_start: 0.6785 (m-30) cc_final: 0.6433 (t0) REVERT: C 314 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8275 (tp40) REVERT: C 558 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8039 (mttm) REVERT: C 658 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7264 (m-40) REVERT: C 675 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7593 (tp40) REVERT: C 985 ASP cc_start: 0.7200 (p0) cc_final: 0.6939 (p0) REVERT: H 34 MET cc_start: 0.3099 (mmm) cc_final: 0.2656 (mmp) REVERT: H 199 THR cc_start: 0.0442 (OUTLIER) cc_final: 0.0016 (m) REVERT: L 169 VAL cc_start: 0.2075 (t) cc_final: 0.1865 (p) REVERT: L 172 THR cc_start: -0.1333 (OUTLIER) cc_final: -0.1562 (t) REVERT: I 123 LYS cc_start: 0.3269 (OUTLIER) cc_final: 0.2531 (mtmm) REVERT: I 176 LEU cc_start: 0.1040 (OUTLIER) cc_final: -0.0169 (pp) REVERT: I 207 LYS cc_start: 0.2996 (OUTLIER) cc_final: 0.1996 (pttt) REVERT: M 159 LYS cc_start: 0.2118 (OUTLIER) cc_final: 0.1745 (tttm) REVERT: M 182 TYR cc_start: 0.2823 (m-80) cc_final: 0.2620 (m-80) outliers start: 235 outliers final: 149 residues processed: 398 average time/residue: 0.4498 time to fit residues: 224.7961 Evaluate side-chains 365 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 191 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS 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 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 207 LYS Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 123 LYS Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 44 SER Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 159 LYS Chi-restraints excluded: chain M residue 163 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 202 SER Chi-restraints excluded: chain M residue 206 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 315 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.5834 > 50:) chunk 39 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 856 ASN A 955 ASN A1002 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C1002 GLN H 177 GLN L 6 GLN ** L 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN ** M 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.206558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.165691 restraints weight = 41268.249| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.21 r_work: 0.3227 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31879 Z= 0.173 Angle : 0.742 14.275 43534 Z= 0.362 Chirality : 0.050 0.539 5097 Planarity : 0.005 0.056 5480 Dihedral : 7.777 85.091 4232 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.36 % Favored : 92.59 % Rotamer: Outliers : 6.41 % Allowed : 23.13 % Favored : 70.46 % 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: -1.46 (0.13), residues: 3804 helix: 0.71 (0.20), residues: 674 sheet: -0.09 (0.15), residues: 1111 loop : -2.17 (0.12), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.022 0.002 TYR B1067 PHE 0.017 0.002 PHE A 898 TRP 0.012 0.001 TRP M 99 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (31763) covalent geometry : angle 0.71183 / 0.35 (43232) SS BOND : bond 0.00462 / 0.26 ( 46) SS BOND : angle 1.87150 / 1.19 ( 92) hydrogen bonds : bond 0.04936 / 3.25 ( 1119) hydrogen bonds : angle 5.44723 / 3.71 ( 3261) link_BETA1-4 : bond 0.00513 / 0.27 ( 22) link_BETA1-4 : angle 2.23893 / 1.39 ( 66) link_NAG-ASN : bond 0.00450 / 0.26 ( 48) link_NAG-ASN : angle 3.14956 / 1.98 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 193 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0544 (mpp) cc_final: -0.2033 (tmm) REVERT: A 158 ARG cc_start: 0.5312 (OUTLIER) cc_final: 0.4673 (mtp-110) REVERT: A 389 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.6305 (m-30) REVERT: A 394 ASN cc_start: 0.5440 (m-40) cc_final: 0.4983 (m-40) REVERT: A 417 LYS cc_start: 0.4953 (OUTLIER) cc_final: 0.4197 (ptmt) REVERT: A 554 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: A 787 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8132 (mm110) REVERT: A 907 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8821 (m110) REVERT: A 960 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8420 (m110) REVERT: A 994 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: A 1142 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7269 (mp-120) REVERT: B 110 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6279 (tp) REVERT: B 224 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: B 355 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6085 (ttp-170) REVERT: B 406 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6362 (mm-30) REVERT: B 473 TYR cc_start: 0.4806 (OUTLIER) cc_final: 0.4071 (m-80) REVERT: B 560 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4974 (mp) REVERT: B 646 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8050 (tmt-80) REVERT: B 787 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8588 (mt0) REVERT: C 28 TYR cc_start: 0.7266 (m-80) cc_final: 0.6623 (m-80) REVERT: C 86 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6155 (t80) REVERT: C 314 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8398 (tp40) REVERT: C 558 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8046 (mttm) REVERT: C 658 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7238 (m-40) REVERT: C 675 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7568 (tp40) REVERT: C 985 ASP cc_start: 0.7209 (p0) cc_final: 0.6943 (p0) REVERT: H 218 GLU cc_start: 0.2597 (OUTLIER) cc_final: 0.2374 (mp0) REVERT: I 123 LYS cc_start: 0.3220 (OUTLIER) cc_final: 0.2467 (mtmm) REVERT: I 176 LEU cc_start: 0.1344 (OUTLIER) cc_final: 0.0196 (pp) REVERT: I 189 THR cc_start: 0.1850 (p) cc_final: 0.1125 (t) REVERT: I 207 LYS cc_start: 0.2792 (OUTLIER) cc_final: 0.1865 (pttt) outliers start: 216 outliers final: 140 residues processed: 386 average time/residue: 0.4529 time to fit residues: 221.1223 Evaluate side-chains 340 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 175 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS 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 554 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 218 GLU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 123 LYS Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 44 SER Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 163 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 202 SER Chi-restraints excluded: chain M residue 206 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 162 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 367 optimal weight: 0.1980 chunk 361 optimal weight: 40.0000 chunk 373 optimal weight: 0.7980 chunk 210 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1002 GLN B 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 914 ASN C 532 ASN C1002 GLN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.208041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.166976 restraints weight = 41504.777| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.22 r_work: 0.3353 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31879 Z= 0.116 Angle : 0.682 12.454 43534 Z= 0.331 Chirality : 0.047 0.441 5097 Planarity : 0.004 0.054 5480 Dihedral : 7.225 87.222 4224 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.81 % Favored : 93.14 % Rotamer: Outliers : 4.96 % Allowed : 24.47 % Favored : 70.58 % 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: -1.16 (0.13), residues: 3804 helix: 1.22 (0.21), residues: 671 sheet: 0.05 (0.15), residues: 1083 loop : -2.02 (0.12), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 237 TYR 0.021 0.001 TYR I 151 PHE 0.014 0.001 PHE B 86 TRP 0.013 0.001 TRP M 99 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (31763) covalent geometry : angle 0.65373 / 0.32 (43232) SS BOND : bond 0.00421 / 0.22 ( 46) SS BOND : angle 1.62032 / 1.01 ( 92) hydrogen bonds : bond 0.03872 / 2.54 ( 1119) hydrogen bonds : angle 5.12725 / 3.49 ( 3261) link_BETA1-4 : bond 0.00776 / 0.46 ( 22) link_BETA1-4 : angle 2.12633 / 1.34 ( 66) link_NAG-ASN : bond 0.00513 / 0.34 ( 48) link_NAG-ASN : angle 2.93479 / 1.78 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 198 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0906 (mpp) cc_final: -0.1723 (tmm) REVERT: A 158 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.4986 (mtp-110) REVERT: A 394 ASN cc_start: 0.5400 (m-40) cc_final: 0.4969 (m110) REVERT: A 417 LYS cc_start: 0.4967 (OUTLIER) cc_final: 0.4294 (ptmt) REVERT: A 588 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 907 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8661 (m110) REVERT: A 1142 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7216 (mp-120) REVERT: B 245 HIS cc_start: 0.6205 (m-70) cc_final: 0.5171 (m-70) REVERT: B 355 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6186 (ttp-170) REVERT: B 406 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6448 (mm-30) REVERT: B 473 TYR cc_start: 0.4762 (OUTLIER) cc_final: 0.4307 (m-80) REVERT: B 560 LEU cc_start: 0.5287 (OUTLIER) cc_final: 0.4998 (mp) REVERT: B 564 GLN cc_start: 0.7334 (mm110) cc_final: 0.6878 (mt0) REVERT: B 787 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8197 (mm-40) REVERT: B 912 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8853 (m) REVERT: C 28 TYR cc_start: 0.7298 (m-80) cc_final: 0.6746 (m-80) REVERT: C 86 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6079 (t80) REVERT: C 235 ILE cc_start: 0.6710 (mt) cc_final: 0.6477 (tt) REVERT: C 314 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8227 (tp40) REVERT: C 417 LYS cc_start: 0.3196 (OUTLIER) cc_final: 0.2919 (tmtp) REVERT: C 558 LYS cc_start: 0.8356 (mtmt) cc_final: 0.8005 (mmmt) REVERT: C 584 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7641 (mp) REVERT: C 675 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7557 (tp40) REVERT: C 985 ASP cc_start: 0.6934 (p0) cc_final: 0.6728 (p0) REVERT: H 34 MET cc_start: 0.3207 (mmm) cc_final: 0.2368 (mmt) REVERT: I 176 LEU cc_start: 0.1155 (OUTLIER) cc_final: 0.0045 (pp) REVERT: I 189 THR cc_start: 0.1710 (OUTLIER) cc_final: 0.0973 (t) REVERT: M 181 LYS cc_start: 0.2869 (OUTLIER) cc_final: 0.1409 (tttm) REVERT: M 196 LYS cc_start: 0.2503 (pttm) cc_final: 0.1558 (mmmt) outliers start: 167 outliers final: 87 residues processed: 349 average time/residue: 0.4901 time to fit residues: 214.3795 Evaluate side-chains 289 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 183 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 44 SER Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 202 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 295 optimal weight: 0.9980 chunk 215 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 382 optimal weight: 8.9990 chunk 357 optimal weight: 30.0000 chunk 274 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 369 optimal weight: 40.0000 chunk 330 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 955 ASN A1002 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B1010 GLN C 532 ASN C1002 GLN C1010 GLN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.204558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.162490 restraints weight = 41150.991| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.31 r_work: 0.3296 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 31879 Z= 0.278 Angle : 0.831 15.993 43534 Z= 0.406 Chirality : 0.055 0.681 5097 Planarity : 0.005 0.070 5480 Dihedral : 7.368 83.227 4200 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.81 % Favored : 92.14 % Rotamer: Outliers : 5.76 % Allowed : 23.66 % Favored : 70.58 % 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: -1.42 (0.13), residues: 3804 helix: 0.68 (0.20), residues: 674 sheet: -0.11 (0.15), residues: 1094 loop : -2.07 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 237 TYR 0.025 0.002 TYR B1067 PHE 0.023 0.003 PHE A 898 TRP 0.019 0.002 TRP A 104 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.28 (31763) covalent geometry : angle 0.79735 / 0.40 (43232) SS BOND : bond 0.00721 / 0.41 ( 46) SS BOND : angle 2.19077 / 1.42 ( 92) hydrogen bonds : bond 0.06037 / 3.99 ( 1119) hydrogen bonds : angle 5.57633 / 3.81 ( 3261) link_BETA1-4 : bond 0.00564 / 0.31 ( 22) link_BETA1-4 : angle 2.53687 / 1.58 ( 66) link_NAG-ASN : bond 0.00553 / 0.29 ( 48) link_NAG-ASN : angle 3.41382 / 2.13 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 185 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0854 (mpp) cc_final: -0.1761 (tmm) REVERT: A 158 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.5157 (mtp-110) REVERT: A 394 ASN cc_start: 0.5423 (m-40) cc_final: 0.5017 (m110) REVERT: A 417 LYS cc_start: 0.5178 (OUTLIER) cc_final: 0.4463 (ptmt) REVERT: A 588 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8635 (p) REVERT: A 907 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8910 (m110) REVERT: A 1142 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7289 (mp-120) REVERT: B 110 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6106 (tp) REVERT: B 314 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: B 355 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6140 (ttp-170) REVERT: B 406 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6408 (mm-30) REVERT: B 473 TYR cc_start: 0.4851 (OUTLIER) cc_final: 0.4472 (m-80) REVERT: B 560 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.5027 (mp) REVERT: B 787 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: C 28 TYR cc_start: 0.7438 (m-80) cc_final: 0.6850 (m-80) REVERT: C 314 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8257 (tp40) REVERT: C 558 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8110 (mttm) REVERT: C 675 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7620 (tp40) REVERT: H 34 MET cc_start: 0.3519 (mmm) cc_final: 0.3020 (mmp) REVERT: H 218 GLU cc_start: 0.2518 (OUTLIER) cc_final: 0.2309 (mp0) REVERT: L 172 THR cc_start: -0.1035 (OUTLIER) cc_final: -0.1291 (t) REVERT: I 176 LEU cc_start: 0.0722 (OUTLIER) cc_final: -0.0172 (pp) REVERT: I 189 THR cc_start: 0.2355 (OUTLIER) cc_final: 0.1449 (t) REVERT: I 207 LYS cc_start: 0.2865 (OUTLIER) cc_final: 0.1858 (pttt) REVERT: M 181 LYS cc_start: 0.2970 (OUTLIER) cc_final: 0.1477 (tttm) outliers start: 194 outliers final: 122 residues processed: 362 average time/residue: 0.4516 time to fit residues: 205.6903 Evaluate side-chains 312 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 170 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 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 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 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 B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 218 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 44 SER Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 202 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 350 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 332 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 234 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN A 544 ASN A 856 ASN A 955 ASN A1002 GLN B 422 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 935 GLN B1010 GLN C 532 ASN C1010 GLN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 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 = 0.4447 r_free = 0.4447 target = 0.206759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.165473 restraints weight = 41428.120| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.28 r_work: 0.3230 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31879 Z= 0.138 Angle : 0.710 14.195 43534 Z= 0.345 Chirality : 0.048 0.573 5097 Planarity : 0.005 0.053 5480 Dihedral : 7.003 84.914 4200 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.62 % Favored : 93.32 % Rotamer: Outliers : 4.51 % Allowed : 24.94 % Favored : 70.55 % 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: -1.17 (0.13), residues: 3804 helix: 1.11 (0.21), residues: 669 sheet: 0.02 (0.15), residues: 1102 loop : -1.97 (0.12), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 237 TYR 0.021 0.001 TYR B1067 PHE 0.016 0.001 PHE B 515 TRP 0.014 0.001 TRP M 99 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (31763) covalent geometry : angle 0.68114 / 0.34 (43232) SS BOND : bond 0.00571 / 0.31 ( 46) SS BOND : angle 1.87038 / 1.22 ( 92) hydrogen bonds : bond 0.04421 / 2.91 ( 1119) hydrogen bonds : angle 5.26108 / 3.59 ( 3261) link_BETA1-4 : bond 0.00552 / 0.30 ( 22) link_BETA1-4 : angle 2.05951 / 1.29 ( 66) link_NAG-ASN : bond 0.00430 / 0.25 ( 48) link_NAG-ASN : angle 2.99577 / 1.86 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 175 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0536 (mpp) cc_final: -0.2040 (tmm) REVERT: A 158 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.4827 (mtp-110) REVERT: A 347 PHE cc_start: 0.6443 (t80) cc_final: 0.6179 (t80) REVERT: A 394 ASN cc_start: 0.5503 (m-40) cc_final: 0.5046 (m110) REVERT: A 417 LYS cc_start: 0.5007 (OUTLIER) cc_final: 0.4268 (ptmt) REVERT: A 588 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8523 (p) REVERT: A 907 ASN cc_start: 0.9036 (OUTLIER) cc_final: 0.8791 (m110) REVERT: A 1142 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7275 (mp-120) REVERT: B 110 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6280 (tp) REVERT: B 224 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: B 245 HIS cc_start: 0.6310 (m-70) cc_final: 0.5258 (m-70) REVERT: B 355 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6092 (ttp-170) REVERT: B 392 PHE cc_start: 0.7692 (m-80) cc_final: 0.7241 (m-80) REVERT: B 406 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: B 473 TYR cc_start: 0.4750 (OUTLIER) cc_final: 0.4294 (m-80) REVERT: B 560 LEU cc_start: 0.5300 (OUTLIER) cc_final: 0.4977 (mp) REVERT: B 614 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7861 (t0) REVERT: B 787 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8605 (mt0) REVERT: B 912 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8888 (m) REVERT: C 28 TYR cc_start: 0.7229 (m-80) cc_final: 0.6663 (m-80) REVERT: C 86 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.5811 (t80) REVERT: C 235 ILE cc_start: 0.6702 (mt) cc_final: 0.6445 (tt) REVERT: C 314 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8419 (tp40) REVERT: C 417 LYS cc_start: 0.3342 (OUTLIER) cc_final: 0.2974 (tmtp) REVERT: C 558 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8028 (mttm) REVERT: C 675 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7523 (tp40) REVERT: C 916 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.8871 (tp) REVERT: H 34 MET cc_start: 0.3704 (mmm) cc_final: 0.3291 (mmp) REVERT: I 176 LEU cc_start: 0.1140 (OUTLIER) cc_final: 0.0072 (pp) REVERT: I 189 THR cc_start: 0.2492 (OUTLIER) cc_final: 0.1614 (t) REVERT: I 207 LYS cc_start: 0.2921 (OUTLIER) cc_final: 0.1953 (pttt) REVERT: M 181 LYS cc_start: 0.2805 (OUTLIER) cc_final: 0.1463 (tttm) outliers start: 152 outliers final: 101 residues processed: 314 average time/residue: 0.4795 time to fit residues: 190.0280 Evaluate side-chains 292 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 168 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 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 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 44 SER Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 202 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 321 optimal weight: 0.3980 chunk 235 optimal weight: 5.9990 chunk 307 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 856 ASN A 955 ASN A 978 ASN A1002 GLN B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 935 GLN B1010 GLN C 532 ASN I 74 ASN ** M 207 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 = 0.4443 r_free = 0.4443 target = 0.206389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.164405 restraints weight = 41222.294| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.29 r_work: 0.3212 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31879 Z= 0.155 Angle : 0.720 14.255 43534 Z= 0.350 Chirality : 0.049 0.556 5097 Planarity : 0.005 0.053 5480 Dihedral : 6.928 83.313 4200 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.36 % Favored : 92.59 % Rotamer: Outliers : 4.48 % Allowed : 24.97 % Favored : 70.55 % 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: -1.08 (0.13), residues: 3804 helix: 1.17 (0.20), residues: 667 sheet: 0.11 (0.15), residues: 1094 loop : -1.93 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 237 TYR 0.024 0.001 TYR L 51 PHE 0.016 0.002 PHE B 515 TRP 0.012 0.001 TRP M 99 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (31763) covalent geometry : angle 0.69196 / 0.34 (43232) SS BOND : bond 0.00568 / 0.32 ( 46) SS BOND : angle 1.79554 / 1.18 ( 92) hydrogen bonds : bond 0.04691 / 3.09 ( 1119) hydrogen bonds : angle 5.24015 / 3.58 ( 3261) link_BETA1-4 : bond 0.00533 / 0.29 ( 22) link_BETA1-4 : angle 2.07598 / 1.29 ( 66) link_NAG-ASN : bond 0.00416 / 0.23 ( 48) link_NAG-ASN : angle 2.99962 / 1.87 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 180 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0365 (mpp) cc_final: -0.2221 (tmm) REVERT: A 158 ARG cc_start: 0.5466 (OUTLIER) cc_final: 0.5017 (mtp-110) REVERT: A 347 PHE cc_start: 0.6415 (t80) cc_final: 0.6195 (t80) REVERT: A 355 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6952 (tpt170) REVERT: A 394 ASN cc_start: 0.5573 (m-40) cc_final: 0.5120 (m110) REVERT: A 417 LYS cc_start: 0.5197 (OUTLIER) cc_final: 0.4388 (ptmt) REVERT: A 588 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8569 (p) REVERT: A 907 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8900 (m110) REVERT: A 1142 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7298 (mp-120) REVERT: B 110 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6289 (tp) REVERT: B 224 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: B 245 HIS cc_start: 0.6318 (m-70) cc_final: 0.5265 (m-70) REVERT: B 355 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6067 (ttp-170) REVERT: B 406 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6290 (mm-30) REVERT: B 473 TYR cc_start: 0.4778 (OUTLIER) cc_final: 0.4484 (m-80) REVERT: B 560 LEU cc_start: 0.5287 (OUTLIER) cc_final: 0.4985 (mp) REVERT: B 614 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7893 (t0) REVERT: B 787 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8596 (mt0) REVERT: C 28 TYR cc_start: 0.7253 (m-80) cc_final: 0.6678 (m-80) REVERT: C 86 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.5797 (t80) REVERT: C 314 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8423 (tp40) REVERT: C 417 LYS cc_start: 0.3446 (OUTLIER) cc_final: 0.3040 (tmtp) REVERT: C 558 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8024 (mttm) REVERT: C 675 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7527 (tp40) REVERT: C 916 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8855 (tp) REVERT: H 34 MET cc_start: 0.3826 (mmm) cc_final: 0.3418 (mmp) REVERT: I 176 LEU cc_start: 0.0796 (OUTLIER) cc_final: -0.0069 (pp) REVERT: I 189 THR cc_start: 0.2556 (OUTLIER) cc_final: 0.1659 (t) REVERT: I 207 LYS cc_start: 0.2906 (OUTLIER) cc_final: 0.1951 (tppt) outliers start: 151 outliers final: 110 residues processed: 317 average time/residue: 0.4765 time to fit residues: 190.2927 Evaluate side-chains 300 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 168 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 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 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 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 B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain L residue 196 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 44 SER Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 301 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 366 optimal weight: 30.0000 chunk 20 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 360 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN A 978 ASN A1002 GLN B 87 ASN B 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B1010 GLN C 481 ASN I 74 ASN I 161 ASN ** M 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.210280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.168012 restraints weight = 40612.576| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.30 r_work: 0.3303 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 31879 Z= 0.213 Angle : 0.774 15.623 43534 Z= 0.378 Chirality : 0.052 0.592 5097 Planarity : 0.005 0.054 5480 Dihedral : 7.129 82.069 4199 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.41 % Favored : 92.53 % Rotamer: Outliers : 4.63 % Allowed : 24.94 % Favored : 70.43 % 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: -1.19 (0.13), residues: 3804 helix: 0.94 (0.20), residues: 667 sheet: 0.08 (0.15), residues: 1088 loop : -1.97 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.025 0.002 TYR C1067 PHE 0.019 0.002 PHE A 898 TRP 0.014 0.002 TRP A 104 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.21 (31763) covalent geometry : angle 0.74333 / 0.37 (43232) SS BOND : bond 0.00645 / 0.36 ( 46) SS BOND : angle 1.92422 / 1.27 ( 92) hydrogen bonds : bond 0.05400 / 3.57 ( 1119) hydrogen bonds : angle 5.40555 / 3.70 ( 3261) link_BETA1-4 : bond 0.00543 / 0.30 ( 22) link_BETA1-4 : angle 2.35219 / 1.46 ( 66) link_NAG-ASN : bond 0.00454 / 0.25 ( 48) link_NAG-ASN : angle 3.23854 / 2.03 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 171 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0435 (mpp) cc_final: -0.2070 (tmm) REVERT: A 158 ARG cc_start: 0.5454 (OUTLIER) cc_final: 0.4979 (mtp-110) REVERT: A 355 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7052 (tpt170) REVERT: A 394 ASN cc_start: 0.5588 (m-40) cc_final: 0.5172 (m110) REVERT: A 417 LYS cc_start: 0.5483 (OUTLIER) cc_final: 0.4507 (tttp) REVERT: A 588 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 960 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8571 (m-40) REVERT: A 1142 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7299 (mp-120) REVERT: B 110 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6119 (mp) REVERT: B 224 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: B 355 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6144 (ttp-170) REVERT: B 406 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6432 (mm-30) REVERT: B 473 TYR cc_start: 0.4874 (OUTLIER) cc_final: 0.4426 (m-80) REVERT: B 560 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.5082 (mp) REVERT: B 787 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8684 (mt0) REVERT: C 28 TYR cc_start: 0.7486 (m-80) cc_final: 0.6949 (m-80) REVERT: C 86 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.5825 (t80) REVERT: C 314 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8514 (tp40) REVERT: C 558 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8117 (mttm) REVERT: C 675 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7638 (tp40) REVERT: C 916 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9003 (tp) REVERT: H 34 MET cc_start: 0.3804 (mmm) cc_final: 0.3333 (mmp) REVERT: L 169 VAL cc_start: 0.2160 (t) cc_final: 0.1689 (p) REVERT: L 203 CYS cc_start: 0.0883 (OUTLIER) cc_final: 0.0490 (m) REVERT: I 176 LEU cc_start: 0.0672 (OUTLIER) cc_final: -0.0195 (pp) REVERT: I 207 LYS cc_start: 0.2969 (OUTLIER) cc_final: 0.2121 (tppt) outliers start: 156 outliers final: 122 residues processed: 313 average time/residue: 0.4989 time to fit residues: 196.8590 Evaluate side-chains 304 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 162 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 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 856 ASN Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 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 B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 196 LYS Chi-restraints excluded: chain L residue 203 CYS Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 44 SER Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 202 SER Chi-restraints excluded: chain M residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 307 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 225 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 274 optimal weight: 0.7980 chunk 263 optimal weight: 0.9990 chunk 311 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 978 ASN A1002 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B1010 GLN ** M 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.205487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.164086 restraints weight = 41365.307| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.23 r_work: 0.3215 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.211 31879 Z= 0.205 Angle : 0.856 59.190 43534 Z= 0.440 Chirality : 0.052 0.912 5097 Planarity : 0.005 0.089 5480 Dihedral : 7.131 82.009 4199 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer: Outliers : 4.45 % Allowed : 25.21 % Favored : 70.34 % 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: -1.20 (0.13), residues: 3804 helix: 0.94 (0.20), residues: 667 sheet: 0.09 (0.15), residues: 1086 loop : -1.98 (0.12), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 237 TYR 0.024 0.002 TYR B1067 PHE 0.018 0.002 PHE B 515 TRP 0.021 0.001 TRP L 158 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (31763) covalent geometry : angle 0.82508 / 0.43 (43232) SS BOND : bond 0.00817 / 0.50 ( 46) SS BOND : angle 2.53161 / 1.55 ( 92) hydrogen bonds : bond 0.05206 / 3.44 ( 1119) hydrogen bonds : angle 5.40115 / 3.70 ( 3261) link_BETA1-4 : bond 0.00591 / 0.33 ( 22) link_BETA1-4 : angle 2.32585 / 1.44 ( 66) link_NAG-ASN : bond 0.00427 / 0.23 ( 48) link_NAG-ASN : angle 3.22746 / 2.02 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10442.70 seconds wall clock time: 178 minutes 51.04 seconds (10731.04 seconds total)