Starting phenix.real_space_refine on Fri Mar 6 20:34:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whd_32499/03_2026/7whd_32499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whd_32499/03_2026/7whd_32499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7whd_32499/03_2026/7whd_32499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whd_32499/03_2026/7whd_32499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7whd_32499/03_2026/7whd_32499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whd_32499/03_2026/7whd_32499.map" } resolution = 2.65 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 ------------------------------------------------------------------------------- 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= 0.002 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 147 5.16 5 C 21677 2.51 5 N 5644 2.21 5 O 6741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34209 Number of models: 1 Model: "" Number of chains: 29 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: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 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: "D" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "H" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "J" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "K" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.44, per 1000 atoms: 0.22 Number of scatterers: 34209 At special positions: 0 Unit cell: (175.664, 164.685, 252.517, 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 147 16.00 O 6741 8.00 N 5644 7.00 C 21677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.49 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.08 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 282 " " NAG A1403 " - " ASN A 603 " " NAG A1404 " - " ASN A 616 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A 165 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 282 " " NAG B1403 " - " ASN B 603 " " NAG B1404 " - " ASN B 616 " " NAG B1405 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 282 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 165 " " NAG F 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.2 seconds 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8054 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 80 sheets defined 18.5% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.969A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.349A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.492A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.178A pdb=" N THR A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.528A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.552A 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 760 through 783 removed outlier: 4.005A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.999A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.667A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.522A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.469A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.892A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.537A 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 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.456A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.692A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.531A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.545A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.577A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.115A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.786A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.714A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.547A pdb=" N GLU B1144 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1145' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.229A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.859A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.520A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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: 3.786A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.117A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.613A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.028A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 976 through 983 removed outlier: 3.622A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.439A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.936A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.055A pdb=" N SER E 127 " --> pdb=" O GLN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.577A pdb=" N GLN G 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.850A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 126 Processing helix chain 'H' and resid 150 through 153 Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.800A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 Processing helix chain 'K' and resid 182 through 188 removed outlier: 3.525A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS K 188 " --> pdb=" O ALA K 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.153A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.708A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.555A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.859A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.936A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.694A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.587A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.123A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.181A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.661A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.126A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 51 through 55 removed outlier: 3.602A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.102A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 225 through 229 removed outlier: 6.757A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 114 through 116 removed outlier: 4.248A pdb=" N THR B 114 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 133 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.409A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.661A 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: 4.347A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 323 through 326 removed outlier: 5.703A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 395 through 402 Processing sheet with id=AD1, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.565A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.837A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.810A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.810A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.436A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.238A pdb=" N GLY C 89 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 50 through 55 removed outlier: 7.474A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.651A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 134 through 135 removed outlier: 6.633A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.453A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.714A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.163A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.176A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.828A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.828A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.978A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 57 through 60 removed outlier: 5.071A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL D 110 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 57 through 60 removed outlier: 5.071A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 92 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 68 through 73 Processing sheet with id=AF8, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.594A pdb=" N GLY D 147 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS D 151 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU D 186 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.594A pdb=" N GLY D 147 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 158 through 162 removed outlier: 3.861A pdb=" N THR D 159 " --> pdb=" O ASN D 207 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 215 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.608A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS E 23 " --> pdb=" O PHE E 71 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.466A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 114 through 118 removed outlier: 6.099A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 144 through 148 Processing sheet with id=AG6, first strand: chain 'G' and resid 3 through 4 removed outlier: 3.862A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.177A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.177A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA G 92 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR G 94 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 68 through 73 Processing sheet with id=AH1, first strand: chain 'G' and resid 128 through 130 removed outlier: 3.533A pdb=" N LYS G 151 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU G 149 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER G 188 " --> pdb=" O LEU G 149 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS G 151 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU G 186 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 144 through 146 removed outlier: 3.651A pdb=" N VAL G 177 " --> pdb=" O SER G 185 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 158 through 162 removed outlier: 3.662A pdb=" N THR G 159 " --> pdb=" O ASN G 207 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.505A pdb=" N SER H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS H 23 " --> pdb=" O PHE H 71 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.683A pdb=" N ARG H 45 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.875A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 145 through 148 removed outlier: 3.530A pdb=" N LYS H 145 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.804A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL J 20 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.640A pdb=" N GLU J 10 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR J 118 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS J 12 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 92 " --> pdb=" O VAL J 117 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL J 93 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.640A pdb=" N GLU J 10 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR J 118 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS J 12 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 92 " --> pdb=" O VAL J 117 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL J 110 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 128 through 130 removed outlier: 6.240A pdb=" N TYR J 184 " --> pdb=" O ASP J 152 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AI4, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AI5, first strand: chain 'K' and resid 18 through 22 removed outlier: 3.551A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 45 through 48 removed outlier: 5.521A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.509A pdb=" N SER K 114 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER K 177 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 153 through 155 removed outlier: 3.813A pdb=" N TRP K 148 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS K 145 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS K 207 " --> pdb=" O CYS K 194 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.99 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10926 1.34 - 1.47: 8730 1.47 - 1.59: 15112 1.59 - 1.71: 0 1.71 - 1.83: 183 Bond restraints: 34951 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C ALA G 102 " pdb=" N PHE G 103 " ideal model delta sigma weight residual 1.332 1.293 0.039 1.40e-02 5.10e+03 7.79e+00 bond pdb=" C1 NAG A1404 " pdb=" O5 NAG A1404 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 ... (remaining 34946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 46294 2.03 - 4.06: 1106 4.06 - 6.09: 110 6.09 - 8.12: 15 8.12 - 10.15: 5 Bond angle restraints: 47530 Sorted by residual: angle pdb=" C ASN A 125 " pdb=" CA ASN A 125 " pdb=" CB ASN A 125 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.70e+01 angle pdb=" CA PHE J 130 " pdb=" C PHE J 130 " pdb=" N PRO J 131 " ideal model delta sigma weight residual 119.06 114.33 4.73 1.05e+00 9.07e-01 2.03e+01 angle pdb=" CA ASN A 125 " pdb=" C ASN A 125 " pdb=" N VAL A 126 " ideal model delta sigma weight residual 119.52 116.30 3.22 7.90e-01 1.60e+00 1.66e+01 angle pdb=" N ASP C 389 " pdb=" CA ASP C 389 " pdb=" C ASP C 389 " ideal model delta sigma weight residual 114.75 109.86 4.89 1.26e+00 6.30e-01 1.51e+01 angle pdb=" N TYR A 380 " pdb=" CA TYR A 380 " pdb=" C TYR A 380 " ideal model delta sigma weight residual 114.75 109.86 4.89 1.26e+00 6.30e-01 1.51e+01 ... (remaining 47525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 19490 17.97 - 35.93: 1645 35.93 - 53.90: 309 53.90 - 71.87: 99 71.87 - 89.83: 40 Dihedral angle restraints: 21583 sinusoidal: 9051 harmonic: 12532 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -175.21 89.21 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 4.38 88.62 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -5.11 -80.89 1 1.00e+01 1.00e-02 8.08e+01 ... (remaining 21580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 5399 0.112 - 0.223: 153 0.223 - 0.334: 6 0.334 - 0.446: 2 0.446 - 0.557: 1 Chirality restraints: 5561 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG B1401 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1401 " pdb=" O5 NAG B1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 5558 not shown) Planarity restraints: 6109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 138 " 0.065 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO B 139 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 139 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 139 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.004 2.00e-02 2.50e+03 3.01e-02 1.13e+01 pdb=" CG ASN A 616 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG A1404 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " -0.022 2.00e-02 2.50e+03 1.85e-02 8.54e+00 pdb=" CG TRP B 64 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.000 2.00e-02 2.50e+03 ... (remaining 6106 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 13 2.22 - 2.89: 14198 2.89 - 3.56: 46062 3.56 - 4.23: 76011 4.23 - 4.90: 130954 Nonbonded interactions: 267238 Sorted by model distance: nonbonded pdb=" CE LYS A 129 " pdb=" CB CYS A 131 " model vdw 1.554 3.840 nonbonded pdb=" CE2 TYR A 660 " pdb=" OE1 GLN A 675 " model vdw 1.889 3.340 nonbonded pdb=" OH TYR B 38 " pdb=" OG1 THR B 284 " model vdw 2.046 3.040 nonbonded pdb=" OD1 ASP C 568 " pdb=" OG1 THR C 572 " model vdw 2.103 3.040 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.124 3.040 ... (remaining 267233 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 620 or resid 641 through 939 or resid 944 throu \ gh 1405)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1405)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1405)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.920 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3516 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 : 0.006 0.459 35056 Z= 0.281 Angle : 0.764 31.160 47794 Z= 0.392 Chirality : 0.049 0.557 5561 Planarity : 0.005 0.100 6072 Dihedral : 14.145 89.832 13376 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.07 % Favored : 90.83 % Rotamer: Outliers : 0.93 % Allowed : 0.93 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -1.88 (0.13), residues: 4265 helix: 1.23 (0.21), residues: 662 sheet: -1.16 (0.15), residues: 1268 loop : -2.10 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 18 TYR 0.034 0.002 TYR A 508 PHE 0.037 0.002 PHE C 906 TRP 0.050 0.002 TRP B 64 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00569 (34951) covalent geometry : angle 0.71327 (47530) SS BOND : bond 0.06473 ( 51) SS BOND : angle 4.43258 ( 102) hydrogen bonds : bond 0.23112 ( 1137) hydrogen bonds : angle 9.16534 ( 3228) link_BETA1-4 : bond 0.00637 ( 17) link_BETA1-4 : angle 1.98983 ( 51) link_NAG-ASN : bond 0.00498 ( 37) link_NAG-ASN : angle 3.72568 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 910 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 139 PRO cc_start: 0.6416 (Cg_endo) cc_final: 0.5393 (Cg_exo) REVERT: A 153 MET cc_start: 0.1620 (mmp) cc_final: 0.0726 (ptp) REVERT: A 197 ILE cc_start: 0.5849 (mp) cc_final: 0.5566 (mp) REVERT: A 726 ILE cc_start: 0.5887 (mp) cc_final: 0.5357 (pt) REVERT: A 781 VAL cc_start: 0.2720 (t) cc_final: 0.2509 (t) REVERT: B 245 HIS cc_start: 0.2519 (m-70) cc_final: 0.0771 (p90) REVERT: B 406 GLU cc_start: 0.4980 (pm20) cc_final: 0.3763 (pp20) REVERT: C 329 PHE cc_start: 0.5358 (m-80) cc_final: 0.4972 (p90) REVERT: C 1027 THR cc_start: 0.0805 (m) cc_final: -0.0271 (p) REVERT: C 1095 PHE cc_start: 0.1286 (m-80) cc_final: 0.0961 (m-80) REVERT: K 210 ASN cc_start: 0.6953 (t0) cc_final: 0.6627 (t0) outliers start: 35 outliers final: 6 residues processed: 935 average time/residue: 0.5273 time to fit residues: 613.5937 Evaluate side-chains 549 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 543 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 160 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 0.0980 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 0.0970 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 542 ASN A 690 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1125 ASN C 66 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN C 955 ASN D 39 GLN E 158 ASN E 210 ASN G 6 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 GLN J 163 ASN ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.118103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.093856 restraints weight = 89931.222| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.51 r_work: 0.3433 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4746 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 35056 Z= 0.178 Angle : 0.823 18.128 47794 Z= 0.402 Chirality : 0.051 0.632 5561 Planarity : 0.005 0.076 6072 Dihedral : 7.502 59.516 5770 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 3.63 % Allowed : 14.67 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -1.76 (0.13), residues: 4265 helix: 1.22 (0.21), residues: 676 sheet: -1.00 (0.14), residues: 1274 loop : -2.06 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 408 TYR 0.022 0.002 TYR B1067 PHE 0.028 0.002 PHE C 135 TRP 0.039 0.002 TRP H 148 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00389 (34951) covalent geometry : angle 0.78859 (47530) SS BOND : bond 0.01562 ( 51) SS BOND : angle 1.78383 ( 102) hydrogen bonds : bond 0.05187 ( 1137) hydrogen bonds : angle 6.61377 ( 3228) link_BETA1-4 : bond 0.00808 ( 17) link_BETA1-4 : angle 2.16329 ( 51) link_NAG-ASN : bond 0.00999 ( 37) link_NAG-ASN : angle 4.49555 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 663 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7631 (OUTLIER) cc_final: 0.7408 (t) REVERT: A 153 MET cc_start: 0.1315 (mmp) cc_final: 0.0280 (ptp) REVERT: A 160 TYR cc_start: 0.5773 (p90) cc_final: 0.5571 (p90) REVERT: A 220 PHE cc_start: 0.4382 (OUTLIER) cc_final: 0.3881 (m-80) REVERT: A 726 ILE cc_start: 0.6794 (mp) cc_final: 0.5983 (pp) REVERT: B 245 HIS cc_start: 0.2941 (m-70) cc_final: 0.1147 (p90) REVERT: B 289 VAL cc_start: 0.4234 (p) cc_final: 0.3950 (m) REVERT: B 394 ASN cc_start: 0.4696 (t0) cc_final: 0.4398 (t0) REVERT: B 691 SER cc_start: 0.4963 (p) cc_final: 0.4509 (m) REVERT: B 770 ILE cc_start: 0.5198 (OUTLIER) cc_final: 0.4707 (mm) REVERT: B 860 VAL cc_start: 0.5733 (p) cc_final: 0.5497 (t) REVERT: C 153 MET cc_start: 0.3308 (ptm) cc_final: 0.2103 (pp-130) REVERT: C 329 PHE cc_start: 0.5403 (m-80) cc_final: 0.4858 (p90) REVERT: C 501 ASN cc_start: 0.5572 (OUTLIER) cc_final: 0.5333 (p0) REVERT: C 731 MET cc_start: 0.5841 (mtp) cc_final: 0.5422 (mtp) REVERT: C 868 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6731 (tp30) REVERT: C 1009 THR cc_start: 0.2292 (t) cc_final: 0.2010 (m) REVERT: C 1027 THR cc_start: 0.2115 (m) cc_final: 0.0892 (p) REVERT: D 146 LEU cc_start: 0.6808 (pp) cc_final: 0.6526 (tt) REVERT: G 103 PHE cc_start: 0.4869 (t80) cc_final: 0.4634 (t80) REVERT: H 148 TRP cc_start: 0.2458 (m100) cc_final: 0.1459 (m100) REVERT: H 185 ASP cc_start: 0.6340 (t0) cc_final: 0.6012 (t70) REVERT: H 188 LYS cc_start: 0.8618 (pptt) cc_final: 0.8344 (pptt) REVERT: J 110 VAL cc_start: 0.6803 (t) cc_final: 0.6281 (p) REVERT: K 4 LEU cc_start: 0.4350 (mp) cc_final: 0.3647 (mt) REVERT: K 39 LYS cc_start: 0.7827 (mmmt) cc_final: 0.6702 (mmmt) REVERT: K 133 VAL cc_start: 0.8397 (p) cc_final: 0.8104 (t) REVERT: K 210 ASN cc_start: 0.8114 (t0) cc_final: 0.7424 (p0) REVERT: K 211 ARG cc_start: 0.8026 (ptm160) cc_final: 0.7520 (ppp80) outliers start: 136 outliers final: 50 residues processed: 738 average time/residue: 0.4989 time to fit residues: 464.7442 Evaluate side-chains 580 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 526 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 782 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 102 optimal weight: 5.9990 chunk 353 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 264 optimal weight: 0.0870 chunk 186 optimal weight: 0.9990 chunk 382 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 414 optimal weight: 10.0000 chunk 386 optimal weight: 6.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 542 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 954 GLN A1083 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 409 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 544 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C1023 ASN C1036 GLN C1113 GLN D 39 GLN G 31 ASN H 6 GLN H 89 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.120184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.096447 restraints weight = 91836.392| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.51 r_work: 0.3502 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5490 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 35056 Z= 0.204 Angle : 0.837 20.081 47794 Z= 0.407 Chirality : 0.051 0.513 5561 Planarity : 0.006 0.077 6072 Dihedral : 7.041 57.787 5759 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.64 % Favored : 93.32 % Rotamer: Outliers : 4.78 % Allowed : 18.70 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -1.69 (0.13), residues: 4265 helix: 1.02 (0.20), residues: 662 sheet: -0.82 (0.15), residues: 1235 loop : -1.99 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 457 TYR 0.030 0.002 TYR A1067 PHE 0.035 0.002 PHE A 377 TRP 0.021 0.002 TRP H 35 HIS 0.006 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00458 (34951) covalent geometry : angle 0.81712 (47530) SS BOND : bond 0.00897 ( 51) SS BOND : angle 1.67854 ( 102) hydrogen bonds : bond 0.04825 ( 1137) hydrogen bonds : angle 6.17061 ( 3228) link_BETA1-4 : bond 0.00947 ( 17) link_BETA1-4 : angle 1.63910 ( 51) link_NAG-ASN : bond 0.00764 ( 37) link_NAG-ASN : angle 3.43129 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 677 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.4787 (p90) cc_final: 0.4261 (p90) REVERT: A 153 MET cc_start: 0.1490 (mmp) cc_final: 0.0255 (ptp) REVERT: A 305 SER cc_start: 0.8843 (t) cc_final: 0.8552 (p) REVERT: A 394 ASN cc_start: 0.6437 (m-40) cc_final: 0.6023 (p0) REVERT: A 438 SER cc_start: 0.6205 (OUTLIER) cc_final: 0.5150 (m) REVERT: A 449 TYR cc_start: 0.4359 (m-80) cc_final: 0.3882 (m-80) REVERT: B 56 LEU cc_start: 0.3052 (tt) cc_final: 0.2425 (tp) REVERT: B 201 PHE cc_start: 0.6570 (t80) cc_final: 0.6326 (t80) REVERT: B 212 LEU cc_start: 0.5650 (pp) cc_final: 0.5070 (tt) REVERT: B 394 ASN cc_start: 0.4931 (t0) cc_final: 0.4702 (t0) REVERT: B 770 ILE cc_start: 0.6291 (mm) cc_final: 0.6014 (mm) REVERT: C 102 ARG cc_start: 0.5732 (mtt90) cc_final: 0.5394 (tpp-160) REVERT: C 153 MET cc_start: 0.3033 (ptm) cc_final: 0.2059 (pp-130) REVERT: C 393 THR cc_start: 0.2333 (OUTLIER) cc_final: 0.2041 (p) REVERT: C 1027 THR cc_start: 0.3554 (m) cc_final: 0.2301 (p) REVERT: C 1095 PHE cc_start: 0.4846 (m-10) cc_final: 0.4441 (m-80) REVERT: D 83 LEU cc_start: 0.7719 (tp) cc_final: 0.7517 (tm) REVERT: E 62 PHE cc_start: 0.2511 (m-10) cc_final: 0.2219 (m-10) REVERT: E 79 GLU cc_start: 0.5277 (mp0) cc_final: 0.4745 (mp0) REVERT: E 186 TYR cc_start: 0.6153 (t80) cc_final: 0.5725 (t80) REVERT: G 222 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.6020 (mptt) REVERT: H 92 SER cc_start: 0.7278 (t) cc_final: 0.7022 (t) REVERT: J 69 THR cc_start: 0.7299 (m) cc_final: 0.7083 (t) REVERT: J 106 TYR cc_start: 0.6390 (t80) cc_final: 0.5446 (t80) REVERT: K 4 LEU cc_start: 0.4679 (mp) cc_final: 0.4097 (mt) REVERT: K 149 LYS cc_start: 0.6693 (mmtt) cc_final: 0.6391 (mmmt) REVERT: K 169 LYS cc_start: 0.7922 (mppt) cc_final: 0.7614 (mppt) REVERT: K 170 ASP cc_start: 0.8268 (t0) cc_final: 0.7753 (OUTLIER) REVERT: K 210 ASN cc_start: 0.8384 (t0) cc_final: 0.7888 (p0) REVERT: K 211 ARG cc_start: 0.8089 (ptm160) cc_final: 0.7533 (ppp80) outliers start: 179 outliers final: 76 residues processed: 790 average time/residue: 0.4921 time to fit residues: 493.7302 Evaluate side-chains 630 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 552 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 782 PHE Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 218 optimal weight: 7.9990 chunk 24 optimal weight: 0.1980 chunk 177 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 93 optimal weight: 0.0770 chunk 50 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 68 optimal weight: 0.0970 chunk 423 optimal weight: 0.0870 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 134 GLN A 498 GLN A 542 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 804 GLN C1005 GLN C1036 GLN C1058 HIS C1113 GLN D 39 GLN E 160 GLN G 31 ASN G 39 GLN H 38 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN K 124 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.117668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.095149 restraints weight = 87615.556| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.29 r_work: 0.3578 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5618 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35056 Z= 0.137 Angle : 0.764 12.292 47794 Z= 0.368 Chirality : 0.048 0.465 5561 Planarity : 0.005 0.075 6072 Dihedral : 6.774 59.553 5759 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.54 % Favored : 93.43 % Rotamer: Outliers : 4.08 % Allowed : 23.43 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -1.48 (0.12), residues: 4265 helix: 1.21 (0.20), residues: 654 sheet: -0.47 (0.15), residues: 1175 loop : -1.95 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 87 TYR 0.024 0.001 TYR D 95 PHE 0.027 0.002 PHE B 92 TRP 0.019 0.002 TRP J 47 HIS 0.006 0.001 HIS K 189 Details of bonding type rmsd covalent geometry : bond 0.00305 (34951) covalent geometry : angle 0.74297 (47530) SS BOND : bond 0.00349 ( 51) SS BOND : angle 1.44040 ( 102) hydrogen bonds : bond 0.04089 ( 1137) hydrogen bonds : angle 5.90345 ( 3228) link_BETA1-4 : bond 0.00763 ( 17) link_BETA1-4 : angle 1.97881 ( 51) link_NAG-ASN : bond 0.00670 ( 37) link_NAG-ASN : angle 3.39442 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 598 time to evaluate : 1.175 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 133 PHE cc_start: 0.4742 (p90) cc_final: 0.4400 (p90) REVERT: A 134 GLN cc_start: 0.6231 (OUTLIER) cc_final: 0.5855 (tp40) REVERT: A 153 MET cc_start: 0.1363 (mmp) cc_final: 0.0079 (ptp) REVERT: A 305 SER cc_start: 0.8832 (t) cc_final: 0.8614 (p) REVERT: A 394 ASN cc_start: 0.6469 (m-40) cc_final: 0.6082 (p0) REVERT: A 998 THR cc_start: 0.7238 (t) cc_final: 0.6920 (p) REVERT: B 201 PHE cc_start: 0.6661 (t80) cc_final: 0.6446 (t80) REVERT: B 1002 GLN cc_start: 0.6407 (tm-30) cc_final: 0.6151 (tm-30) REVERT: C 153 MET cc_start: 0.3235 (ptm) cc_final: 0.2588 (ptt) REVERT: C 306 PHE cc_start: 0.5095 (OUTLIER) cc_final: 0.4549 (m-10) REVERT: C 329 PHE cc_start: 0.5188 (m-80) cc_final: 0.4402 (p90) REVERT: C 393 THR cc_start: 0.2615 (OUTLIER) cc_final: 0.1930 (p) REVERT: C 642 VAL cc_start: 0.5075 (OUTLIER) cc_final: 0.4776 (t) REVERT: C 730 SER cc_start: 0.7642 (OUTLIER) cc_final: 0.7419 (m) REVERT: C 1027 THR cc_start: 0.3408 (m) cc_final: 0.2265 (p) REVERT: C 1077 THR cc_start: 0.6418 (t) cc_final: 0.5942 (m) REVERT: D 83 LEU cc_start: 0.7679 (tp) cc_final: 0.7216 (tm) REVERT: D 132 LEU cc_start: 0.6888 (mm) cc_final: 0.6644 (mp) REVERT: D 197 LEU cc_start: 0.8869 (mm) cc_final: 0.8428 (pp) REVERT: E 62 PHE cc_start: 0.2168 (m-10) cc_final: 0.1878 (m-10) REVERT: G 222 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5888 (mptt) REVERT: J 3 GLN cc_start: 0.7044 (mm110) cc_final: 0.6597 (tp40) REVERT: J 69 THR cc_start: 0.7364 (m) cc_final: 0.7084 (t) REVERT: J 152 ASP cc_start: 0.8724 (t0) cc_final: 0.8509 (t0) REVERT: K 4 LEU cc_start: 0.4792 (mp) cc_final: 0.4342 (mt) REVERT: K 149 LYS cc_start: 0.6666 (mmtt) cc_final: 0.6285 (mmmt) REVERT: K 169 LYS cc_start: 0.7989 (mppt) cc_final: 0.7720 (mppt) REVERT: K 170 ASP cc_start: 0.8169 (t0) cc_final: 0.7529 (t0) REVERT: K 186 TYR cc_start: 0.8319 (t80) cc_final: 0.7731 (t80) REVERT: K 210 ASN cc_start: 0.8334 (t0) cc_final: 0.7912 (p0) REVERT: K 211 ARG cc_start: 0.8145 (ptm160) cc_final: 0.7114 (ppp80) outliers start: 153 outliers final: 64 residues processed: 687 average time/residue: 0.4705 time to fit residues: 416.0279 Evaluate side-chains 596 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 526 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 782 PHE Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 384 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 335 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 110 optimal weight: 0.0030 chunk 28 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 421 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 536 ASN A 644 GLN A 804 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN B1142 GLN C 409 GLN C 460 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 751 ASN C 901 GLN E 37 GLN G 31 ASN J 62 GLN J 163 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.121753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.099705 restraints weight = 92893.019| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.37 r_work: 0.3634 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 1.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.201 35056 Z= 0.395 Angle : 1.237 24.495 47794 Z= 0.622 Chirality : 0.063 0.756 5561 Planarity : 0.009 0.175 6072 Dihedral : 8.046 59.974 5759 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.38 % Favored : 90.50 % Rotamer: Outliers : 7.55 % Allowed : 21.69 % Favored : 70.76 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.10 % 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: -2.61 (0.12), residues: 4265 helix: -0.66 (0.18), residues: 686 sheet: -1.05 (0.14), residues: 1240 loop : -2.53 (0.11), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG D 38 TYR 0.044 0.004 TYR C 741 PHE 0.047 0.004 PHE A 497 TRP 0.052 0.005 TRP D 111 HIS 0.017 0.003 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00903 (34951) covalent geometry : angle 1.21156 (47530) SS BOND : bond 0.00930 ( 51) SS BOND : angle 2.56990 ( 102) hydrogen bonds : bond 0.07351 ( 1137) hydrogen bonds : angle 7.08636 ( 3228) link_BETA1-4 : bond 0.00815 ( 17) link_BETA1-4 : angle 3.60554 ( 51) link_NAG-ASN : bond 0.01792 ( 37) link_NAG-ASN : angle 4.31257 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 283 poor density : 746 time to evaluate : 1.287 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: 0.1422 (mmp) cc_final: 0.0318 (ptp) REVERT: A 203 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8143 (mm) REVERT: A 305 SER cc_start: 0.8922 (t) cc_final: 0.8570 (p) REVERT: A 332 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.6819 (mp) REVERT: A 394 ASN cc_start: 0.7355 (m-40) cc_final: 0.6939 (p0) REVERT: A 417 LYS cc_start: 0.7870 (tppp) cc_final: 0.7638 (tppt) REVERT: A 421 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6947 (p90) REVERT: A 455 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8438 (pp) REVERT: A 516 GLU cc_start: 0.5871 (tm-30) cc_final: 0.5401 (tm-30) REVERT: A 661 GLU cc_start: 0.8207 (mp0) cc_final: 0.7907 (mm-30) REVERT: A 950 ASP cc_start: 0.8142 (m-30) cc_final: 0.7926 (m-30) REVERT: A 998 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8158 (p) REVERT: B 509 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6999 (mtt-85) REVERT: B 699 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8711 (tp) REVERT: B 710 ASN cc_start: 0.7860 (t0) cc_final: 0.7590 (t0) REVERT: B 765 ARG cc_start: 0.8522 (tpt-90) cc_final: 0.8111 (ttm-80) REVERT: B 784 GLN cc_start: 0.7939 (mt0) cc_final: 0.7737 (mt0) REVERT: B 950 ASP cc_start: 0.7881 (m-30) cc_final: 0.7567 (m-30) REVERT: B 954 GLN cc_start: 0.7909 (mt0) cc_final: 0.7646 (pt0) REVERT: B 992 GLN cc_start: 0.7371 (mm-40) cc_final: 0.7137 (mt0) REVERT: C 51 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7462 (m) REVERT: C 153 MET cc_start: 0.3390 (ptm) cc_final: 0.2381 (pp-130) REVERT: C 194 PHE cc_start: 0.8332 (m-80) cc_final: 0.8122 (m-80) REVERT: C 267 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7182 (t) REVERT: C 508 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6569 (t80) REVERT: C 642 VAL cc_start: 0.6992 (OUTLIER) cc_final: 0.6653 (t) REVERT: C 656 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8057 (p) REVERT: C 663 ASP cc_start: 0.6645 (t70) cc_final: 0.6199 (t0) REVERT: C 664 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7366 (mt) REVERT: C 773 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7764 (tt0) REVERT: C 1019 ARG cc_start: 0.8273 (ptm-80) cc_final: 0.7750 (tmm160) REVERT: C 1111 GLU cc_start: 0.8744 (pp20) cc_final: 0.8434 (pp20) REVERT: D 82 GLU cc_start: 0.6392 (tm-30) cc_final: 0.6165 (tm-30) REVERT: D 163 ASN cc_start: 0.8124 (m-40) cc_final: 0.7856 (m-40) REVERT: E 17 GLU cc_start: 0.7788 (pt0) cc_final: 0.7466 (pm20) REVERT: E 39 LYS cc_start: 0.6840 (ptpt) cc_final: 0.6599 (mtmm) REVERT: E 42 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6880 (tp-100) REVERT: E 75 ILE cc_start: 0.6540 (mm) cc_final: 0.6058 (mm) REVERT: E 82 ASP cc_start: 0.8298 (m-30) cc_final: 0.7378 (m-30) REVERT: E 102 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8408 (p) REVERT: E 142 ARG cc_start: 0.7719 (tpt90) cc_final: 0.7473 (tmm160) REVERT: E 183 LYS cc_start: 0.8955 (ptmm) cc_final: 0.8637 (ptpp) REVERT: G 10 GLU cc_start: 0.7846 (tp30) cc_final: 0.7592 (tm-30) REVERT: G 205 ASN cc_start: 0.7269 (p0) cc_final: 0.7009 (p0) REVERT: G 222 LYS cc_start: 0.6603 (OUTLIER) cc_final: 0.6365 (mptt) REVERT: H 185 ASP cc_start: 0.7046 (t70) cc_final: 0.6713 (t0) REVERT: H 188 LYS cc_start: 0.9013 (pptt) cc_final: 0.8678 (pptt) REVERT: H 189 HIS cc_start: 0.7374 (m170) cc_final: 0.6874 (m-70) REVERT: J 32 TYR cc_start: 0.6135 (m-80) cc_final: 0.5437 (m-80) REVERT: J 69 THR cc_start: 0.7706 (m) cc_final: 0.7391 (t) REVERT: K 47 LEU cc_start: 0.7587 (mt) cc_final: 0.7256 (mm) REVERT: K 82 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.5885 (t0) REVERT: K 89 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7527 (pp30) REVERT: K 149 LYS cc_start: 0.6641 (mmtt) cc_final: 0.6158 (mmmt) REVERT: K 170 ASP cc_start: 0.8488 (t0) cc_final: 0.7726 (t0) outliers start: 283 outliers final: 75 residues processed: 935 average time/residue: 0.5912 time to fit residues: 678.9909 Evaluate side-chains 596 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 503 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 163 ASN Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 4 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 371 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 180 optimal weight: 0.4980 chunk 338 optimal weight: 0.7980 chunk 210 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 363 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 644 GLN A 954 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 414 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B1119 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN E 199 GLN G 31 ASN H 53 ASN ** H 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.143003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.124293 restraints weight = 101600.967| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.64 r_work: 0.3657 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 1.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35056 Z= 0.171 Angle : 0.876 17.218 47794 Z= 0.425 Chirality : 0.052 0.800 5561 Planarity : 0.006 0.104 6072 Dihedral : 7.201 59.777 5759 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.52 % Favored : 93.46 % Rotamer: Outliers : 3.87 % Allowed : 28.98 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.03 (0.12), residues: 4265 helix: 0.51 (0.20), residues: 676 sheet: -0.90 (0.14), residues: 1272 loop : -2.25 (0.12), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 995 TYR 0.033 0.002 TYR A 380 PHE 0.029 0.002 PHE A 497 TRP 0.025 0.002 TRP J 47 HIS 0.014 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00384 (34951) covalent geometry : angle 0.85227 (47530) SS BOND : bond 0.00599 ( 51) SS BOND : angle 2.52526 ( 102) hydrogen bonds : bond 0.04805 ( 1137) hydrogen bonds : angle 6.16896 ( 3228) link_BETA1-4 : bond 0.00815 ( 17) link_BETA1-4 : angle 2.10473 ( 51) link_NAG-ASN : bond 0.00532 ( 37) link_NAG-ASN : angle 3.34263 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 583 time to evaluate : 1.302 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: 0.1338 (mmp) cc_final: 0.0397 (ptp) REVERT: A 298 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6912 (mp0) REVERT: A 305 SER cc_start: 0.8917 (t) cc_final: 0.8623 (p) REVERT: A 332 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6482 (mp) REVERT: A 378 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6298 (ttpp) REVERT: A 661 GLU cc_start: 0.8289 (mp0) cc_final: 0.7980 (tm-30) REVERT: A 755 GLN cc_start: 0.7575 (tp-100) cc_final: 0.7343 (tp-100) REVERT: A 858 LEU cc_start: 0.8043 (tt) cc_final: 0.7482 (mp) REVERT: A 869 MET cc_start: 0.8949 (mpp) cc_final: 0.8514 (mtm) REVERT: A 921 LYS cc_start: 0.8039 (pmtt) cc_final: 0.7740 (ptpp) REVERT: A 950 ASP cc_start: 0.8265 (m-30) cc_final: 0.8038 (m-30) REVERT: A 954 GLN cc_start: 0.8564 (mt0) cc_final: 0.8355 (mt0) REVERT: A 1010 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8850 (mm110) REVERT: B 138 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6694 (p0) REVERT: B 414 GLN cc_start: 0.6341 (OUTLIER) cc_final: 0.5798 (mt0) REVERT: B 509 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6917 (mmm-85) REVERT: B 571 ASP cc_start: 0.6012 (t0) cc_final: 0.5730 (p0) REVERT: B 697 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8400 (ttm) REVERT: B 756 TYR cc_start: 0.8377 (m-80) cc_final: 0.8082 (m-80) REVERT: B 950 ASP cc_start: 0.8097 (m-30) cc_final: 0.7825 (m-30) REVERT: C 91 TYR cc_start: 0.4184 (t80) cc_final: 0.3379 (t80) REVERT: C 153 MET cc_start: 0.3559 (ptm) cc_final: 0.2838 (ptt) REVERT: C 239 GLN cc_start: 0.7127 (tt0) cc_final: 0.6855 (tp40) REVERT: C 267 VAL cc_start: 0.7314 (p) cc_final: 0.6911 (t) REVERT: C 314 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8285 (tm-30) REVERT: C 508 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6181 (t80) REVERT: C 663 ASP cc_start: 0.6775 (t70) cc_final: 0.6465 (t0) REVERT: C 756 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7705 (t80) REVERT: C 1019 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.8232 (tmm160) REVERT: C 1031 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: D 64 PHE cc_start: 0.7513 (t80) cc_final: 0.7082 (t80) REVERT: D 152 ASP cc_start: 0.8622 (t0) cc_final: 0.8340 (m-30) REVERT: D 197 LEU cc_start: 0.8921 (mm) cc_final: 0.8629 (pp) REVERT: D 203 ILE cc_start: 0.7135 (mp) cc_final: 0.6838 (tp) REVERT: E 17 GLU cc_start: 0.7822 (pt0) cc_final: 0.7585 (mp0) REVERT: E 18 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7876 (mmm-85) REVERT: E 39 LYS cc_start: 0.6946 (ptpt) cc_final: 0.6608 (mtmm) REVERT: E 54 ARG cc_start: 0.9078 (tmm-80) cc_final: 0.8730 (tmm-80) REVERT: E 82 ASP cc_start: 0.8173 (m-30) cc_final: 0.7386 (m-30) REVERT: E 142 ARG cc_start: 0.7972 (tpt90) cc_final: 0.7740 (tmm160) REVERT: G 10 GLU cc_start: 0.7823 (tp30) cc_final: 0.7257 (tm-30) REVERT: G 222 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6151 (mptt) REVERT: H 17 GLU cc_start: 0.7748 (mp0) cc_final: 0.7219 (mp0) REVERT: H 185 ASP cc_start: 0.6894 (t70) cc_final: 0.6616 (t0) REVERT: H 188 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8659 (pptt) REVERT: H 189 HIS cc_start: 0.7472 (m170) cc_final: 0.7012 (m-70) REVERT: J 69 THR cc_start: 0.7923 (m) cc_final: 0.7608 (t) REVERT: J 87 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7031 (mpt180) REVERT: J 163 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8777 (p0) REVERT: K 123 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8278 (pp20) REVERT: K 149 LYS cc_start: 0.6741 (mmtt) cc_final: 0.6358 (mmmt) REVERT: K 169 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8378 (mppt) REVERT: K 170 ASP cc_start: 0.8472 (t0) cc_final: 0.7668 (t0) outliers start: 145 outliers final: 51 residues processed: 684 average time/residue: 0.5699 time to fit residues: 480.8513 Evaluate side-chains 536 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 472 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 163 ASN Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 384 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 399 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 233 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 703 ASN A1005 GLN B 207 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B1005 GLN B1142 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN D 200 GLN E 138 ASN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 GLN G 31 ASN H 53 ASN H 89 GLN J 163 ASN K 210 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.114450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.089211 restraints weight = 89657.800| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.40 r_work: 0.3449 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 1.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 35056 Z= 0.222 Angle : 0.878 15.561 47794 Z= 0.428 Chirality : 0.052 0.582 5561 Planarity : 0.006 0.110 6072 Dihedral : 7.051 58.800 5759 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.97 % Favored : 92.00 % Rotamer: Outliers : 4.00 % Allowed : 30.12 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.87 (0.12), residues: 4265 helix: 0.84 (0.20), residues: 673 sheet: -0.89 (0.14), residues: 1265 loop : -2.15 (0.12), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 408 TYR 0.033 0.002 TYR C 91 PHE 0.037 0.002 PHE A 562 TRP 0.029 0.003 TRP J 47 HIS 0.011 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00528 (34951) covalent geometry : angle 0.85783 (47530) SS BOND : bond 0.00569 ( 51) SS BOND : angle 2.23474 ( 102) hydrogen bonds : bond 0.04990 ( 1137) hydrogen bonds : angle 5.95866 ( 3228) link_BETA1-4 : bond 0.00439 ( 17) link_BETA1-4 : angle 2.05622 ( 51) link_NAG-ASN : bond 0.00591 ( 37) link_NAG-ASN : angle 3.15447 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 500 time to evaluate : 1.295 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 153 MET cc_start: 0.1118 (mmp) cc_final: 0.0270 (ptp) REVERT: A 298 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6915 (mp0) REVERT: A 393 THR cc_start: 0.8018 (m) cc_final: 0.7801 (p) REVERT: A 417 LYS cc_start: 0.8075 (tptt) cc_final: 0.7535 (tppt) REVERT: A 421 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6693 (p90) REVERT: A 428 ASP cc_start: 0.7755 (t0) cc_final: 0.7386 (p0) REVERT: A 462 LYS cc_start: 0.8542 (mtpp) cc_final: 0.7667 (mmtt) REVERT: A 516 GLU cc_start: 0.6586 (tm-30) cc_final: 0.6080 (tm-30) REVERT: A 934 ILE cc_start: 0.8765 (tp) cc_final: 0.8541 (tp) REVERT: A 950 ASP cc_start: 0.8210 (m-30) cc_final: 0.7924 (m-30) REVERT: B 84 LEU cc_start: 0.6519 (tt) cc_final: 0.5891 (mt) REVERT: B 135 PHE cc_start: 0.4722 (OUTLIER) cc_final: 0.4252 (p90) REVERT: B 138 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6868 (p0) REVERT: B 229 LEU cc_start: 0.7861 (mm) cc_final: 0.7462 (tt) REVERT: B 237 ARG cc_start: 0.6424 (mtm-85) cc_final: 0.6143 (mpp80) REVERT: B 508 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.4862 (m-80) REVERT: B 509 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7056 (mmm-85) REVERT: B 571 ASP cc_start: 0.6150 (t0) cc_final: 0.5800 (p0) REVERT: B 867 ASP cc_start: 0.8717 (p0) cc_final: 0.8085 (m-30) REVERT: B 868 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7837 (tp30) REVERT: B 877 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8475 (mt) REVERT: C 92 PHE cc_start: 0.7665 (t80) cc_final: 0.7436 (t80) REVERT: C 153 MET cc_start: 0.3459 (ptm) cc_final: 0.2744 (ptt) REVERT: C 226 LEU cc_start: 0.7689 (tp) cc_final: 0.7414 (tm) REVERT: C 239 GLN cc_start: 0.7148 (tt0) cc_final: 0.6880 (tt0) REVERT: C 329 PHE cc_start: 0.7566 (m-80) cc_final: 0.7222 (m-80) REVERT: C 508 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6633 (t80) REVERT: C 710 ASN cc_start: 0.8606 (m-40) cc_final: 0.7777 (p0) REVERT: C 756 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: C 1115 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7862 (mt) REVERT: D 152 ASP cc_start: 0.8708 (t0) cc_final: 0.8425 (m-30) REVERT: D 197 LEU cc_start: 0.9042 (mm) cc_final: 0.8733 (pp) REVERT: D 207 ASN cc_start: 0.8665 (t0) cc_final: 0.8335 (m-40) REVERT: E 17 GLU cc_start: 0.8214 (pt0) cc_final: 0.7955 (pm20) REVERT: E 82 ASP cc_start: 0.8498 (m-30) cc_final: 0.7537 (m-30) REVERT: E 132 VAL cc_start: 0.8867 (t) cc_final: 0.8620 (m) REVERT: G 10 GLU cc_start: 0.7815 (tp30) cc_final: 0.7598 (tp30) REVERT: G 179 GLN cc_start: 0.9048 (mp10) cc_final: 0.8752 (mp10) REVERT: G 222 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6608 (mptt) REVERT: H 91 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8578 (mtp-110) REVERT: H 180 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8603 (p) REVERT: H 181 LEU cc_start: 0.8140 (mp) cc_final: 0.7885 (mm) REVERT: H 188 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8648 (pptt) REVERT: J 32 TYR cc_start: 0.5478 (m-80) cc_final: 0.5200 (m-80) REVERT: J 69 THR cc_start: 0.8034 (m) cc_final: 0.7783 (t) REVERT: J 87 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7011 (mpt180) REVERT: K 11 LEU cc_start: 0.8118 (tp) cc_final: 0.7772 (mp) REVERT: K 170 ASP cc_start: 0.8494 (t0) cc_final: 0.7794 (t0) outliers start: 150 outliers final: 78 residues processed: 605 average time/residue: 0.5402 time to fit residues: 405.5592 Evaluate side-chains 525 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 434 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 10 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 115 optimal weight: 0.0010 chunk 368 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 644 GLN B 207 HIS B 422 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1005 GLN C 409 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN E 158 ASN G 31 ASN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 89 GLN K 210 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.115254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.090182 restraints weight = 88944.767| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.38 r_work: 0.3448 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 1.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35056 Z= 0.156 Angle : 0.838 14.109 47794 Z= 0.408 Chirality : 0.050 0.533 5561 Planarity : 0.005 0.082 6072 Dihedral : 6.787 57.818 5759 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 3.12 % Allowed : 31.38 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.70 (0.12), residues: 4265 helix: 1.03 (0.20), residues: 663 sheet: -0.74 (0.14), residues: 1254 loop : -2.06 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 319 TYR 0.032 0.002 TYR H 140 PHE 0.027 0.002 PHE D 103 TRP 0.029 0.002 TRP K 148 HIS 0.012 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00363 (34951) covalent geometry : angle 0.81980 (47530) SS BOND : bond 0.00532 ( 51) SS BOND : angle 2.29412 ( 102) hydrogen bonds : bond 0.04331 ( 1137) hydrogen bonds : angle 5.72392 ( 3228) link_BETA1-4 : bond 0.00533 ( 17) link_BETA1-4 : angle 1.85060 ( 51) link_NAG-ASN : bond 0.00455 ( 37) link_NAG-ASN : angle 2.85930 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 474 time to evaluate : 1.320 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: 0.1149 (mmp) cc_final: 0.0394 (ptp) REVERT: A 298 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6923 (mp0) REVERT: A 332 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6812 (mp) REVERT: A 417 LYS cc_start: 0.7959 (tptt) cc_final: 0.7450 (tppt) REVERT: A 421 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6546 (p90) REVERT: A 428 ASP cc_start: 0.7751 (t0) cc_final: 0.7357 (p0) REVERT: A 516 GLU cc_start: 0.6558 (tm-30) cc_final: 0.6286 (tm-30) REVERT: A 755 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7493 (tp-100) REVERT: A 914 ASN cc_start: 0.8022 (t0) cc_final: 0.7730 (t0) REVERT: A 921 LYS cc_start: 0.8358 (pmtt) cc_final: 0.8053 (ptpp) REVERT: A 934 ILE cc_start: 0.8659 (tp) cc_final: 0.8403 (tp) REVERT: A 950 ASP cc_start: 0.8126 (m-30) cc_final: 0.7856 (m-30) REVERT: A 1096 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9054 (t) REVERT: B 84 LEU cc_start: 0.6636 (tt) cc_final: 0.6130 (mt) REVERT: B 138 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6974 (p0) REVERT: B 229 LEU cc_start: 0.7811 (mm) cc_final: 0.7427 (tt) REVERT: B 237 ARG cc_start: 0.6462 (mtm-85) cc_final: 0.6162 (mpp80) REVERT: B 508 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.4988 (m-80) REVERT: B 509 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6972 (mmm-85) REVERT: B 867 ASP cc_start: 0.8660 (p0) cc_final: 0.8052 (m-30) REVERT: B 868 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7746 (tp30) REVERT: B 877 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8472 (mt) REVERT: B 933 LYS cc_start: 0.8372 (mmpt) cc_final: 0.8116 (mmmm) REVERT: B 1031 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: C 92 PHE cc_start: 0.7617 (t80) cc_final: 0.7322 (t80) REVERT: C 153 MET cc_start: 0.3460 (ptm) cc_final: 0.2893 (ptt) REVERT: C 226 LEU cc_start: 0.7662 (tp) cc_final: 0.7442 (tm) REVERT: C 239 GLN cc_start: 0.7250 (tt0) cc_final: 0.7049 (tt0) REVERT: C 329 PHE cc_start: 0.7389 (m-80) cc_final: 0.7041 (m-80) REVERT: C 508 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6506 (t80) REVERT: C 710 ASN cc_start: 0.8610 (m-40) cc_final: 0.7910 (p0) REVERT: C 756 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: D 152 ASP cc_start: 0.8643 (t0) cc_final: 0.8337 (m-30) REVERT: D 197 LEU cc_start: 0.8976 (mm) cc_final: 0.8671 (pp) REVERT: D 207 ASN cc_start: 0.8598 (t0) cc_final: 0.8246 (m-40) REVERT: E 82 ASP cc_start: 0.8482 (m-30) cc_final: 0.7738 (m-30) REVERT: E 132 VAL cc_start: 0.8921 (t) cc_final: 0.8678 (m) REVERT: E 145 LYS cc_start: 0.7634 (tppt) cc_final: 0.7090 (ttpp) REVERT: E 147 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7383 (tp40) REVERT: E 183 LYS cc_start: 0.9068 (ptmm) cc_final: 0.8802 (ptpp) REVERT: G 106 TYR cc_start: 0.8836 (t80) cc_final: 0.8479 (t80) REVERT: G 108 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7498 (mtt) REVERT: G 222 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6306 (mptt) REVERT: H 17 GLU cc_start: 0.7782 (mp0) cc_final: 0.7395 (mp0) REVERT: H 91 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8653 (mtp-110) REVERT: H 181 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7931 (mm) REVERT: J 32 TYR cc_start: 0.5344 (m-80) cc_final: 0.5108 (m-80) REVERT: J 69 THR cc_start: 0.7991 (m) cc_final: 0.7764 (t) REVERT: J 96 CYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7566 (p) REVERT: K 123 GLU cc_start: 0.9096 (tp30) cc_final: 0.8070 (pp20) REVERT: K 170 ASP cc_start: 0.8487 (t0) cc_final: 0.8273 (t0) REVERT: K 195 GLU cc_start: 0.7076 (tp30) cc_final: 0.6511 (tp30) outliers start: 117 outliers final: 56 residues processed: 557 average time/residue: 0.5575 time to fit residues: 385.0503 Evaluate side-chains 507 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 435 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 83 optimal weight: 0.7980 chunk 312 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 275 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 316 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 389 optimal weight: 0.7980 chunk 348 optimal weight: 1.9990 chunk 196 optimal weight: 0.2980 chunk 226 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1142 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN E 147 GLN G 31 ASN H 53 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.115532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.090251 restraints weight = 89273.149| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.41 r_work: 0.3468 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 1.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35056 Z= 0.149 Angle : 0.835 13.685 47794 Z= 0.404 Chirality : 0.050 0.538 5561 Planarity : 0.005 0.083 6072 Dihedral : 6.517 57.869 5759 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.03 % Favored : 92.92 % Rotamer: Outliers : 2.83 % Allowed : 31.94 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -1.57 (0.12), residues: 4265 helix: 1.10 (0.21), residues: 656 sheet: -0.60 (0.14), residues: 1249 loop : -2.00 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 319 TYR 0.023 0.001 TYR C 508 PHE 0.042 0.002 PHE A 562 TRP 0.040 0.002 TRP K 148 HIS 0.013 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00346 (34951) covalent geometry : angle 0.81827 (47530) SS BOND : bond 0.00399 ( 51) SS BOND : angle 2.10743 ( 102) hydrogen bonds : bond 0.04060 ( 1137) hydrogen bonds : angle 5.54384 ( 3228) link_BETA1-4 : bond 0.00652 ( 17) link_BETA1-4 : angle 1.85694 ( 51) link_NAG-ASN : bond 0.00459 ( 37) link_NAG-ASN : angle 2.76342 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 488 time to evaluate : 1.367 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: 0.1273 (mmp) cc_final: 0.0531 (pmt) REVERT: A 298 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6978 (mp0) REVERT: A 332 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6710 (mp) REVERT: A 393 THR cc_start: 0.8039 (m) cc_final: 0.7779 (p) REVERT: A 421 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.6627 (p90) REVERT: A 428 ASP cc_start: 0.7950 (t0) cc_final: 0.7442 (p0) REVERT: A 483 VAL cc_start: 0.7480 (t) cc_final: 0.7274 (p) REVERT: A 516 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6118 (tm-30) REVERT: A 755 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7579 (tp-100) REVERT: A 934 ILE cc_start: 0.8620 (tp) cc_final: 0.8325 (tp) REVERT: A 950 ASP cc_start: 0.8058 (m-30) cc_final: 0.7808 (m-30) REVERT: A 1010 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8740 (mm110) REVERT: A 1096 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9075 (t) REVERT: B 84 LEU cc_start: 0.6602 (tt) cc_final: 0.6371 (mt) REVERT: B 138 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6926 (p0) REVERT: B 170 TYR cc_start: 0.5054 (OUTLIER) cc_final: 0.4762 (t80) REVERT: B 229 LEU cc_start: 0.7851 (mm) cc_final: 0.7465 (tt) REVERT: B 237 ARG cc_start: 0.6543 (mtm-85) cc_final: 0.6243 (mpp80) REVERT: B 867 ASP cc_start: 0.8648 (p0) cc_final: 0.8049 (m-30) REVERT: B 868 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7700 (tp30) REVERT: B 877 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 933 LYS cc_start: 0.8362 (mmpt) cc_final: 0.8160 (mmmt) REVERT: B 994 ASP cc_start: 0.8482 (m-30) cc_final: 0.7903 (t0) REVERT: C 92 PHE cc_start: 0.7842 (t80) cc_final: 0.7514 (t80) REVERT: C 153 MET cc_start: 0.3421 (ptm) cc_final: 0.2881 (ptt) REVERT: C 226 LEU cc_start: 0.7792 (tp) cc_final: 0.7575 (tm) REVERT: C 239 GLN cc_start: 0.7259 (tt0) cc_final: 0.7052 (tt0) REVERT: C 329 PHE cc_start: 0.7536 (m-80) cc_final: 0.7185 (m-80) REVERT: C 392 PHE cc_start: 0.6767 (m-80) cc_final: 0.6468 (m-80) REVERT: C 508 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6893 (t80) REVERT: C 710 ASN cc_start: 0.8617 (m-40) cc_final: 0.7910 (p0) REVERT: C 756 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8516 (m-80) REVERT: D 30 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7606 (m) REVERT: D 152 ASP cc_start: 0.8700 (t0) cc_final: 0.8397 (m-30) REVERT: D 197 LEU cc_start: 0.9026 (mm) cc_final: 0.8701 (pp) REVERT: D 207 ASN cc_start: 0.8611 (t0) cc_final: 0.8224 (m-40) REVERT: E 10 THR cc_start: 0.7871 (p) cc_final: 0.7561 (t) REVERT: E 82 ASP cc_start: 0.8458 (m-30) cc_final: 0.7839 (m-30) REVERT: E 103 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8335 (tmtt) REVERT: E 145 LYS cc_start: 0.7736 (tppt) cc_final: 0.7035 (ttpp) REVERT: E 147 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: E 183 LYS cc_start: 0.9041 (ptmm) cc_final: 0.8807 (ptpp) REVERT: E 195 GLU cc_start: 0.8012 (pp20) cc_final: 0.7756 (pp20) REVERT: G 3 GLN cc_start: 0.8441 (mp10) cc_final: 0.8231 (mm110) REVERT: G 10 GLU cc_start: 0.7709 (tp30) cc_final: 0.7335 (tm-30) REVERT: G 106 TYR cc_start: 0.8843 (t80) cc_final: 0.8523 (t80) REVERT: G 203 ILE cc_start: 0.8854 (pp) cc_final: 0.8198 (tp) REVERT: G 222 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6232 (mptt) REVERT: H 17 GLU cc_start: 0.7651 (mp0) cc_final: 0.7426 (mp0) REVERT: H 91 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8709 (mtp-110) REVERT: H 105 GLU cc_start: 0.7912 (pm20) cc_final: 0.7634 (pm20) REVERT: H 183 LYS cc_start: 0.7447 (mmmm) cc_final: 0.7155 (mtpp) REVERT: J 32 TYR cc_start: 0.5439 (m-80) cc_final: 0.5146 (m-80) REVERT: J 69 THR cc_start: 0.8087 (m) cc_final: 0.7819 (t) REVERT: J 87 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.6557 (mpt180) REVERT: J 220 GLU cc_start: 0.7732 (pp20) cc_final: 0.7523 (tm-30) REVERT: K 123 GLU cc_start: 0.9193 (tp30) cc_final: 0.8156 (pp20) REVERT: K 170 ASP cc_start: 0.8871 (t0) cc_final: 0.8191 (t0) REVERT: K 195 GLU cc_start: 0.7138 (tp30) cc_final: 0.6582 (tp30) outliers start: 106 outliers final: 57 residues processed: 562 average time/residue: 0.5562 time to fit residues: 387.6146 Evaluate side-chains 508 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 438 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 39 optimal weight: 0.0070 chunk 412 optimal weight: 0.0000 chunk 186 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 chunk 347 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 405 optimal weight: 0.0870 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A1005 GLN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN D 39 GLN D 163 ASN E 147 GLN E 158 ASN G 31 ASN H 53 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.115643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.090528 restraints weight = 89711.965| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.40 r_work: 0.3476 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 1.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35056 Z= 0.146 Angle : 0.842 14.702 47794 Z= 0.409 Chirality : 0.050 0.539 5561 Planarity : 0.005 0.082 6072 Dihedral : 6.371 57.089 5759 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.08 % Favored : 92.90 % Rotamer: Outliers : 2.29 % Allowed : 32.63 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -1.48 (0.13), residues: 4265 helix: 1.13 (0.21), residues: 661 sheet: -0.50 (0.14), residues: 1267 loop : -1.96 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 319 TYR 0.029 0.001 TYR E 140 PHE 0.034 0.001 PHE B 562 TRP 0.044 0.002 TRP J 47 HIS 0.013 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00338 (34951) covalent geometry : angle 0.82657 (47530) SS BOND : bond 0.00414 ( 51) SS BOND : angle 2.04896 ( 102) hydrogen bonds : bond 0.03916 ( 1137) hydrogen bonds : angle 5.45741 ( 3228) link_BETA1-4 : bond 0.00672 ( 17) link_BETA1-4 : angle 1.79096 ( 51) link_NAG-ASN : bond 0.00447 ( 37) link_NAG-ASN : angle 2.69145 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 473 time to evaluate : 1.366 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: 0.1285 (mmp) cc_final: 0.0549 (pmt) REVERT: A 195 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8122 (mtmt) REVERT: A 332 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6689 (mp) REVERT: A 417 LYS cc_start: 0.8095 (tptt) cc_final: 0.7729 (tptt) REVERT: A 421 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.6520 (p90) REVERT: A 428 ASP cc_start: 0.7946 (t0) cc_final: 0.7420 (p0) REVERT: A 483 VAL cc_start: 0.7237 (t) cc_final: 0.7007 (p) REVERT: A 516 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6381 (tm-30) REVERT: A 755 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7633 (tp-100) REVERT: A 934 ILE cc_start: 0.8553 (tp) cc_final: 0.8255 (tp) REVERT: A 950 ASP cc_start: 0.8050 (m-30) cc_final: 0.7809 (m-30) REVERT: A 1005 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8185 (tp40) REVERT: A 1010 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8790 (mm110) REVERT: A 1096 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9080 (t) REVERT: B 84 LEU cc_start: 0.6698 (tt) cc_final: 0.6476 (mt) REVERT: B 138 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7167 (p0) REVERT: B 229 LEU cc_start: 0.7880 (mm) cc_final: 0.7464 (tt) REVERT: B 237 ARG cc_start: 0.6598 (mtm-85) cc_final: 0.6298 (mpp80) REVERT: B 867 ASP cc_start: 0.8621 (p0) cc_final: 0.8040 (m-30) REVERT: B 868 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7695 (tp30) REVERT: B 933 LYS cc_start: 0.8333 (mmpt) cc_final: 0.8126 (mmmt) REVERT: B 994 ASP cc_start: 0.8556 (m-30) cc_final: 0.7890 (t0) REVERT: C 92 PHE cc_start: 0.7699 (t80) cc_final: 0.7473 (t80) REVERT: C 153 MET cc_start: 0.3528 (ptm) cc_final: 0.3054 (ptt) REVERT: C 329 PHE cc_start: 0.7532 (m-80) cc_final: 0.7173 (m-80) REVERT: C 392 PHE cc_start: 0.6820 (m-80) cc_final: 0.6527 (m-80) REVERT: C 473 TYR cc_start: 0.7648 (t80) cc_final: 0.7444 (t80) REVERT: C 508 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6985 (t80) REVERT: C 552 LEU cc_start: 0.9211 (tm) cc_final: 0.8845 (mm) REVERT: C 663 ASP cc_start: 0.6381 (t70) cc_final: 0.6148 (t0) REVERT: C 710 ASN cc_start: 0.8612 (m-40) cc_final: 0.7905 (p0) REVERT: C 1031 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: D 64 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7023 (t80) REVERT: D 152 ASP cc_start: 0.8715 (t0) cc_final: 0.8395 (m-30) REVERT: D 197 LEU cc_start: 0.9015 (mm) cc_final: 0.8693 (pp) REVERT: D 207 ASN cc_start: 0.8606 (t0) cc_final: 0.8266 (m-40) REVERT: E 10 THR cc_start: 0.7944 (p) cc_final: 0.7618 (t) REVERT: E 82 ASP cc_start: 0.8555 (m-30) cc_final: 0.7870 (m-30) REVERT: E 103 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8362 (tmtt) REVERT: E 132 VAL cc_start: 0.8838 (m) cc_final: 0.8597 (t) REVERT: E 145 LYS cc_start: 0.7625 (tppt) cc_final: 0.6949 (ttpp) REVERT: E 147 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: E 183 LYS cc_start: 0.9066 (ptmm) cc_final: 0.8831 (ptpp) REVERT: E 195 GLU cc_start: 0.8019 (pp20) cc_final: 0.7783 (pp20) REVERT: G 3 GLN cc_start: 0.8454 (mp10) cc_final: 0.8208 (mm110) REVERT: G 10 GLU cc_start: 0.7798 (tp30) cc_final: 0.7384 (tm-30) REVERT: G 106 TYR cc_start: 0.8824 (t80) cc_final: 0.8562 (t80) REVERT: G 203 ILE cc_start: 0.8837 (pp) cc_final: 0.8169 (tp) REVERT: G 222 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6308 (mptt) REVERT: H 17 GLU cc_start: 0.7726 (mp0) cc_final: 0.7508 (mp0) REVERT: H 183 LYS cc_start: 0.7440 (mmmm) cc_final: 0.7206 (mtpp) REVERT: J 32 TYR cc_start: 0.5469 (m-80) cc_final: 0.5198 (m-80) REVERT: J 67 ARG cc_start: 0.7723 (mtp180) cc_final: 0.7184 (ptm160) REVERT: J 69 THR cc_start: 0.8080 (m) cc_final: 0.7861 (t) REVERT: J 70 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6274 (mt) REVERT: K 2 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6728 (mp) REVERT: K 28 SER cc_start: 0.8329 (m) cc_final: 0.8126 (t) REVERT: K 89 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7261 (pp30) REVERT: K 123 GLU cc_start: 0.9174 (tp30) cc_final: 0.8171 (pp20) REVERT: K 124 GLN cc_start: 0.7459 (tm130) cc_final: 0.6798 (tm-30) REVERT: K 170 ASP cc_start: 0.8868 (t0) cc_final: 0.8218 (t0) outliers start: 86 outliers final: 56 residues processed: 536 average time/residue: 0.5654 time to fit residues: 377.9800 Evaluate side-chains 511 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 440 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 98 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 316 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 414 optimal weight: 1.9990 chunk 273 optimal weight: 0.4980 chunk 364 optimal weight: 6.9990 chunk 372 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN A 422 ASN A 644 GLN B 49 HIS B 207 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN D 163 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN H 53 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.112556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.086693 restraints weight = 88500.107| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.41 r_work: 0.3371 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 1.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35056 Z= 0.196 Angle : 0.890 12.697 47794 Z= 0.436 Chirality : 0.052 0.636 5561 Planarity : 0.006 0.081 6072 Dihedral : 6.557 58.829 5759 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.55 % Favored : 92.40 % Rotamer: Outliers : 2.64 % Allowed : 32.71 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.55 (0.13), residues: 4265 helix: 1.08 (0.20), residues: 661 sheet: -0.75 (0.14), residues: 1325 loop : -1.89 (0.12), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 408 TYR 0.024 0.002 TYR G 184 PHE 0.047 0.002 PHE A 562 TRP 0.030 0.003 TRP J 47 HIS 0.012 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00462 (34951) covalent geometry : angle 0.87265 (47530) SS BOND : bond 0.00546 ( 51) SS BOND : angle 2.20263 ( 102) hydrogen bonds : bond 0.04780 ( 1137) hydrogen bonds : angle 5.59816 ( 3228) link_BETA1-4 : bond 0.00525 ( 17) link_BETA1-4 : angle 1.92576 ( 51) link_NAG-ASN : bond 0.00482 ( 37) link_NAG-ASN : angle 2.98458 ( 111) =============================================================================== Job complete usr+sys time: 17564.45 seconds wall clock time: 298 minutes 24.13 seconds (17904.13 seconds total)