Starting phenix.real_space_refine on Mon Jul 6 09:12:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7whd_32499/07_2026/7whd_32499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whd_32499/07_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_32499/07_2026/7whd_32499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whd_32499/07_2026/7whd_32499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7whd_32499/07_2026/7whd_32499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whd_32499/07_2026/7whd_32499.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7whd_32499/07_2026/7whd_32499.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7whd_32499/07_2026/7whd_32499.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 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 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 chiralities: 8 Time building chain proxies: 6.48, per 1000 atoms: 0.19 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: 2.83 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: 1.15 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: 9.10 Time building geometry restraints manager: 3.76 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: 18491 17.97 - 35.93: 1594 35.93 - 53.90: 257 53.90 - 71.87: 67 71.87 - 89.83: 40 Dihedral angle restraints: 20449 sinusoidal: 7917 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 20446 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.170 Find NCS groups from input model: 0.960 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:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3507 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 : 14.035 89.832 12242 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/Z covalent geometry : bond 0.00569 / 0.25 (34951) covalent geometry : angle 0.71327 / 0.38 (47530) SS BOND : bond 0.06473 / 4.70 ( 51) SS BOND : angle 4.43258 / 3.31 ( 102) hydrogen bonds : bond 0.23112 / 14.70 ( 1137) hydrogen bonds : angle 9.16534 / 6.26 ( 3228) link_BETA1-4 : bond 0.00637 / 0.42 ( 17) link_BETA1-4 : angle 1.98983 / 1.24 ( 51) link_NAG-ASN : bond 0.00498 / 0.29 ( 37) link_NAG-ASN : angle 3.72568 / 2.59 ( 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 : 1.130 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: 0.5161 time to fit residues: 604.3429 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 : 1.212 ------------------------------------------------------------------------------- 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... 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 613 GLN B 955 ASN 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 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.118429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.094219 restraints weight = 90038.547| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.51 r_work: 0.3428 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4764 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35056 Z= 0.177 Angle : 0.855 20.748 47794 Z= 0.416 Chirality : 0.051 0.567 5561 Planarity : 0.006 0.075 6072 Dihedral : 4.925 30.141 4636 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.32 % Rotamer: Outliers : 3.82 % Allowed : 14.62 % Favored : 81.56 % 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: -1.79 (0.13), residues: 4265 helix: 1.11 (0.20), residues: 678 sheet: -1.00 (0.15), residues: 1260 loop : -2.07 (0.12), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 408 TYR 0.025 0.002 TYR B1067 PHE 0.026 0.002 PHE K 209 TRP 0.043 0.003 TRP H 148 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (34951) covalent geometry : angle 0.82209 / 0.41 (47530) SS BOND : bond 0.00556 / 0.37 ( 51) SS BOND : angle 1.78718 / 1.14 ( 102) hydrogen bonds : bond 0.04797 / 3.12 ( 1137) hydrogen bonds : angle 6.53816 / 4.47 ( 3228) link_BETA1-4 : bond 0.00683 / 0.46 ( 17) link_BETA1-4 : angle 2.25325 / 1.37 ( 51) link_NAG-ASN : bond 0.00678 / 0.31 ( 37) link_NAG-ASN : angle 4.49879 / 3.55 ( 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 817 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 674 time to evaluate : 1.141 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: A 126 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7485 (t) REVERT: A 153 MET cc_start: 0.1323 (mmp) cc_final: 0.0275 (ptp) REVERT: A 189 LEU cc_start: 0.6858 (mt) cc_final: 0.6612 (mt) REVERT: A 220 PHE cc_start: 0.4421 (OUTLIER) cc_final: 0.3947 (m-80) REVERT: A 720 ILE cc_start: 0.1028 (OUTLIER) cc_final: 0.0659 (tp) REVERT: B 237 ARG cc_start: 0.4417 (mtm-85) cc_final: 0.4172 (mpp80) REVERT: B 245 HIS cc_start: 0.3004 (m-70) cc_final: 0.1149 (p90) REVERT: B 289 VAL cc_start: 0.4332 (p) cc_final: 0.4038 (m) REVERT: B 394 ASN cc_start: 0.4658 (t0) cc_final: 0.4400 (t0) REVERT: B 691 SER cc_start: 0.5459 (p) cc_final: 0.4994 (m) REVERT: B 770 ILE cc_start: 0.5204 (OUTLIER) cc_final: 0.4652 (mm) REVERT: B 860 VAL cc_start: 0.6079 (p) cc_final: 0.5836 (t) REVERT: C 153 MET cc_start: 0.3462 (ptm) cc_final: 0.2317 (pp-130) REVERT: C 329 PHE cc_start: 0.5399 (m-80) cc_final: 0.4887 (p90) REVERT: C 501 ASN cc_start: 0.5671 (OUTLIER) cc_final: 0.5432 (p0) REVERT: C 731 MET cc_start: 0.5828 (mtp) cc_final: 0.5435 (mtp) REVERT: C 1009 THR cc_start: 0.2471 (t) cc_final: 0.2195 (m) REVERT: C 1027 THR cc_start: 0.2258 (m) cc_final: 0.0983 (p) REVERT: G 103 PHE cc_start: 0.4735 (t80) cc_final: 0.4508 (t80) REVERT: H 117 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6784 (pp) REVERT: H 148 TRP cc_start: 0.2449 (m100) cc_final: 0.1800 (m100) REVERT: J 73 ASP cc_start: 0.7556 (t0) cc_final: 0.7355 (p0) REVERT: J 110 VAL cc_start: 0.6784 (t) cc_final: 0.6298 (p) REVERT: K 4 LEU cc_start: 0.4321 (mp) cc_final: 0.3608 (mt) REVERT: K 210 ASN cc_start: 0.8127 (t0) cc_final: 0.7476 (p0) REVERT: K 211 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7530 (ppp80) outliers start: 143 outliers final: 53 residues processed: 750 average time/residue: 0.5043 time to fit residues: 480.2134 Evaluate side-chains 587 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 528 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 465 GLU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 720 ILE 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 159 VAL 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 4 LEU 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 H residue 117 ILE Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain J residue 16 SER 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 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: 3.9990 chunk 353 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 175 optimal weight: 0.0980 chunk 136 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 382 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 414 optimal weight: 9.9990 chunk 386 optimal weight: 7.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 954 GLN A1083 HIS A1106 GLN ** 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 501 ASN C 540 ASN C 544 ASN C 764 ASN C1023 ASN C1036 GLN C1113 GLN D 39 GLN G 31 ASN G 39 GLN H 6 GLN H 38 GLN H 89 GLN J 163 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.141293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.122790 restraints weight = 99450.900| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.56 r_work: 0.3576 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 35056 Z= 0.214 Angle : 0.856 22.138 47794 Z= 0.419 Chirality : 0.051 0.440 5561 Planarity : 0.006 0.107 6072 Dihedral : 4.852 26.954 4625 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.85 % Favored : 93.13 % Rotamer: Outliers : 5.15 % Allowed : 18.78 % Favored : 76.07 % 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: -1.73 (0.12), residues: 4265 helix: 0.85 (0.20), residues: 655 sheet: -0.72 (0.15), residues: 1189 loop : -2.02 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG C 457 TYR 0.032 0.002 TYR A1067 PHE 0.031 0.002 PHE B 377 TRP 0.047 0.003 TRP E 35 HIS 0.013 0.002 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (34951) covalent geometry : angle 0.83530 / 0.41 (47530) SS BOND : bond 0.00779 / 0.43 ( 51) SS BOND : angle 1.81148 / 1.29 ( 102) hydrogen bonds : bond 0.04929 / 3.23 ( 1137) hydrogen bonds : angle 6.23333 / 4.26 ( 3228) link_BETA1-4 : bond 0.00706 / 0.45 ( 17) link_BETA1-4 : angle 1.64220 / 1.01 ( 51) link_NAG-ASN : bond 0.01001 / 0.62 ( 37) link_NAG-ASN : angle 3.50255 / 2.52 ( 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 892 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 699 time to evaluate : 1.290 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: A 133 PHE cc_start: 0.4735 (p90) cc_final: 0.4332 (p90) REVERT: A 153 MET cc_start: 0.1567 (mmp) cc_final: 0.0236 (ptp) REVERT: A 305 SER cc_start: 0.8865 (t) cc_final: 0.8575 (p) REVERT: A 394 ASN cc_start: 0.6523 (m-40) cc_final: 0.6249 (p0) REVERT: A 438 SER cc_start: 0.6509 (OUTLIER) cc_final: 0.6244 (m) REVERT: A 449 TYR cc_start: 0.4565 (m-80) cc_final: 0.4104 (m-80) REVERT: A 788 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5983 (tp) REVERT: A 902 MET cc_start: 0.4807 (OUTLIER) cc_final: 0.4569 (tpp) REVERT: B 56 LEU cc_start: 0.3122 (tt) cc_final: 0.2615 (tp) REVERT: B 770 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.6101 (mm) REVERT: C 153 MET cc_start: 0.3337 (ptm) cc_final: 0.2128 (pp-130) REVERT: C 571 ASP cc_start: 0.6417 (m-30) cc_final: 0.6055 (p0) REVERT: C 866 THR cc_start: 0.6784 (p) cc_final: 0.6504 (p) REVERT: C 869 MET cc_start: 0.7421 (ttm) cc_final: 0.7201 (ttm) REVERT: C 1009 THR cc_start: 0.4794 (t) cc_final: 0.2859 (p) REVERT: C 1095 PHE cc_start: 0.5520 (m-10) cc_final: 0.5089 (m-80) REVERT: C 1133 VAL cc_start: 0.7506 (OUTLIER) cc_final: 0.7305 (t) REVERT: E 62 PHE cc_start: 0.2259 (m-10) cc_final: 0.1979 (m-10) REVERT: E 79 GLU cc_start: 0.5695 (mp0) cc_final: 0.5233 (mp0) REVERT: H 181 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6029 (pp) REVERT: H 188 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8412 (pptt) REVERT: J 73 ASP cc_start: 0.7689 (t0) cc_final: 0.7477 (p0) REVERT: J 80 TYR cc_start: 0.7269 (m-80) cc_final: 0.6892 (m-80) REVERT: J 99 GLU cc_start: 0.5344 (tm-30) cc_final: 0.5111 (tm-30) REVERT: J 106 TYR cc_start: 0.6449 (t80) cc_final: 0.5720 (t80) REVERT: K 4 LEU cc_start: 0.4838 (mp) cc_final: 0.4379 (mt) REVERT: K 63 ILE cc_start: 0.6087 (OUTLIER) cc_final: 0.5727 (pp) REVERT: K 82 ASP cc_start: 0.4772 (OUTLIER) cc_final: 0.4387 (t70) REVERT: K 149 LYS cc_start: 0.6698 (mmtt) cc_final: 0.6280 (mmmt) REVERT: K 170 ASP cc_start: 0.8157 (t0) cc_final: 0.7616 (t0) REVERT: K 210 ASN cc_start: 0.8284 (t0) cc_final: 0.7837 (p0) REVERT: K 211 ARG cc_start: 0.8143 (ptm160) cc_final: 0.7594 (ppp80) outliers start: 193 outliers final: 81 residues processed: 820 average time/residue: 0.5031 time to fit residues: 524.1484 Evaluate side-chains 655 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 565 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 267 VAL Chi-restraints excluded: chain A residue 430 THR 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 788 ILE Chi-restraints excluded: chain A residue 902 MET 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 1137 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 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 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 595 VAL 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 697 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 770 ILE 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 B residue 1133 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER 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 312 ILE Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL 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 1133 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 118 PHE 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 140 SER Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain G residue 211 SER 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 181 LEU Chi-restraints excluded: chain H residue 188 LYS 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 63 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: 3.9990 chunk 177 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 193 optimal weight: 0.0980 chunk 176 optimal weight: 0.9980 chunk 93 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 423 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 644 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 414 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1142 GLN C 487 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 872 GLN C1005 GLN C1036 GLN C1113 GLN C1135 ASN D 39 GLN E 160 GLN G 31 ASN ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN ** J 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.142761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.124645 restraints weight = 100086.236| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.58 r_work: 0.3609 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 35056 Z= 0.173 Angle : 0.786 16.315 47794 Z= 0.385 Chirality : 0.049 0.416 5561 Planarity : 0.005 0.074 6072 Dihedral : 4.719 26.422 4625 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.68 % Favored : 93.29 % Rotamer: Outliers : 4.99 % Allowed : 23.29 % Favored : 71.72 % 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: -1.62 (0.12), residues: 4265 helix: 1.02 (0.20), residues: 663 sheet: -0.70 (0.14), residues: 1242 loop : -1.97 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 24 TYR 0.025 0.002 TYR C 265 PHE 0.028 0.002 PHE C 392 TRP 0.031 0.002 TRP E 35 HIS 0.007 0.001 HIS K 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (34951) covalent geometry : angle 0.77068 / 0.38 (47530) SS BOND : bond 0.00496 / 0.35 ( 51) SS BOND : angle 1.62084 / 1.07 ( 102) hydrogen bonds : bond 0.04249 / 2.78 ( 1137) hydrogen bonds : angle 5.90263 / 4.06 ( 3228) link_BETA1-4 : bond 0.00856 / 0.54 ( 17) link_BETA1-4 : angle 1.76516 / 1.10 ( 51) link_NAG-ASN : bond 0.00613 / 0.35 ( 37) link_NAG-ASN : angle 2.81637 / 2.16 ( 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 833 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 646 time to evaluate : 1.229 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: A 153 MET cc_start: 0.1305 (mmp) cc_final: -0.0010 (ptp) REVERT: A 195 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7876 (mttt) REVERT: A 305 SER cc_start: 0.8862 (t) cc_final: 0.8607 (p) REVERT: A 394 ASN cc_start: 0.6760 (m-40) cc_final: 0.6493 (p0) REVERT: A 602 THR cc_start: 0.7106 (t) cc_final: 0.6838 (m) REVERT: A 998 THR cc_start: 0.7583 (t) cc_final: 0.7275 (p) REVERT: A 1132 ILE cc_start: 0.7037 (mp) cc_final: 0.6832 (mp) REVERT: B 201 PHE cc_start: 0.6540 (t80) cc_final: 0.6220 (t80) REVERT: B 406 GLU cc_start: 0.6428 (pm20) cc_final: 0.5837 (pm20) REVERT: B 613 GLN cc_start: 0.5513 (OUTLIER) cc_final: 0.5286 (mt0) REVERT: B 740 MET cc_start: 0.6200 (mtp) cc_final: 0.5998 (mtt) REVERT: B 867 ASP cc_start: 0.7687 (p0) cc_final: 0.7142 (m-30) REVERT: C 153 MET cc_start: 0.3333 (ptm) cc_final: 0.2640 (ptt) REVERT: C 486 PHE cc_start: 0.7744 (p90) cc_final: 0.7460 (p90) REVERT: C 487 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7810 (p0) REVERT: C 505 TYR cc_start: 0.6847 (t80) cc_final: 0.6630 (t80) REVERT: C 571 ASP cc_start: 0.6492 (m-30) cc_final: 0.6249 (p0) REVERT: C 666 ILE cc_start: 0.5476 (mt) cc_final: 0.5130 (mt) REVERT: C 730 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.7300 (m) REVERT: C 775 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6691 (m-30) REVERT: C 1009 THR cc_start: 0.5509 (t) cc_final: 0.3717 (p) REVERT: C 1036 GLN cc_start: 0.5945 (OUTLIER) cc_final: 0.5713 (tt0) REVERT: C 1058 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.5720 (t-90) REVERT: C 1133 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.7424 (t) REVERT: D 64 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6711 (t80) REVERT: D 197 LEU cc_start: 0.8870 (mm) cc_final: 0.8411 (pp) REVERT: D 222 LYS cc_start: 0.4292 (mptt) cc_final: 0.3883 (mptt) REVERT: E 62 PHE cc_start: 0.2581 (m-10) cc_final: 0.2335 (m-10) REVERT: H 185 ASP cc_start: 0.6622 (t70) cc_final: 0.6273 (t70) REVERT: H 188 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8469 (pptt) REVERT: J 73 ASP cc_start: 0.7961 (t0) cc_final: 0.7636 (p0) REVERT: J 80 TYR cc_start: 0.7224 (m-80) cc_final: 0.6881 (m-80) REVERT: J 87 ARG cc_start: 0.7440 (mtm110) cc_final: 0.6691 (mpt180) REVERT: K 4 LEU cc_start: 0.4882 (mp) cc_final: 0.4519 (mt) REVERT: K 82 ASP cc_start: 0.5010 (OUTLIER) cc_final: 0.4452 (t0) REVERT: K 169 LYS cc_start: 0.7851 (mppt) cc_final: 0.7381 (mmtm) REVERT: K 170 ASP cc_start: 0.8096 (t0) cc_final: 0.7478 (t0) REVERT: K 186 TYR cc_start: 0.8199 (t80) cc_final: 0.7953 (t80) REVERT: K 210 ASN cc_start: 0.8262 (t0) cc_final: 0.7936 (p0) REVERT: K 211 ARG cc_start: 0.8118 (ptm160) cc_final: 0.7306 (ppp80) outliers start: 187 outliers final: 80 residues processed: 764 average time/residue: 0.4639 time to fit residues: 458.7555 Evaluate side-chains 654 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 563 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL 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 915 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 394 ASN 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 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 782 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 135 PHE 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 387 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 ILE 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 775 ASP Chi-restraints excluded: chain C residue 1036 GLN Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1058 HIS 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 C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 75 SER 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 5 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 384 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 335 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 245 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 421 optimal weight: 6.9990 chunk 301 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 644 GLN A 784 GLN A 804 GLN A 928 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 450 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B1036 GLN B1142 GLN C 487 ASN C 501 ASN C 607 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN D 200 GLN E 138 ASN H 124 GLN J 65 GLN J 163 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.120800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.097894 restraints weight = 92000.012| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.47 r_work: 0.3594 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 1.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.212 35056 Z= 0.282 Angle : 1.026 16.846 47794 Z= 0.513 Chirality : 0.057 0.556 5561 Planarity : 0.008 0.174 6072 Dihedral : 5.761 29.864 4625 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.53 % Favored : 91.35 % Rotamer: Outliers : 7.18 % Allowed : 23.03 % Favored : 69.80 % Cbeta Deviations : 0.05 % 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: -2.21 (0.12), residues: 4265 helix: -0.11 (0.19), residues: 689 sheet: -0.90 (0.14), residues: 1267 loop : -2.29 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 102 TYR 0.031 0.003 TYR C 279 PHE 0.041 0.003 PHE C 464 TRP 0.065 0.004 TRP E 35 HIS 0.018 0.003 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.28 (34951) covalent geometry : angle 1.00850 / 0.51 (47530) SS BOND : bond 0.01002 / 0.69 ( 51) SS BOND : angle 2.31603 / 1.39 ( 102) hydrogen bonds : bond 0.06088 / 4.00 ( 1137) hydrogen bonds : angle 6.45018 / 4.42 ( 3228) link_BETA1-4 : bond 0.01129 / 0.74 ( 17) link_BETA1-4 : angle 2.32218 / 1.43 ( 51) link_NAG-ASN : bond 0.01324 / 0.79 ( 37) link_NAG-ASN : angle 3.26097 / 2.30 ( 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 1008 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 739 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1370 (mmp) cc_final: 0.0265 (ptp) REVERT: A 203 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7884 (mm) REVERT: A 305 SER cc_start: 0.8915 (t) cc_final: 0.8568 (p) REVERT: A 314 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 421 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6621 (p90) REVERT: A 455 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8028 (pp) REVERT: A 602 THR cc_start: 0.7879 (t) cc_final: 0.7482 (m) REVERT: A 642 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7864 (t) REVERT: A 900 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7901 (mmm) REVERT: A 994 ASP cc_start: 0.7745 (t0) cc_final: 0.7525 (t70) REVERT: A 998 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.8010 (p) REVERT: A 1001 LEU cc_start: 0.8859 (tm) cc_final: 0.8648 (tp) REVERT: A 1141 LEU cc_start: 0.8917 (tp) cc_final: 0.8687 (OUTLIER) REVERT: B 335 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7747 (tm) REVERT: B 347 PHE cc_start: 0.6524 (m-10) cc_final: 0.6270 (m-10) REVERT: B 405 ASP cc_start: 0.8624 (p0) cc_final: 0.8324 (m-30) REVERT: B 470 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7665 (p) REVERT: B 539 VAL cc_start: 0.8559 (m) cc_final: 0.8252 (p) REVERT: B 710 ASN cc_start: 0.7248 (t0) cc_final: 0.7012 (t0) REVERT: B 740 MET cc_start: 0.7910 (mtp) cc_final: 0.7672 (mtp) REVERT: B 992 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7116 (mt0) REVERT: B 995 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.7636 (mtp85) REVERT: C 153 MET cc_start: 0.3445 (ptm) cc_final: 0.2674 (ptt) REVERT: C 306 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.7124 (m-10) REVERT: C 312 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7381 (tt) REVERT: C 329 PHE cc_start: 0.6599 (m-80) cc_final: 0.5145 (p90) REVERT: C 611 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7043 (tp) REVERT: C 642 VAL cc_start: 0.5995 (OUTLIER) cc_final: 0.5684 (t) REVERT: C 660 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7185 (m-80) REVERT: C 664 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6708 (mt) REVERT: C 780 GLU cc_start: 0.8262 (tp30) cc_final: 0.8061 (tp30) REVERT: C 873 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6422 (t80) REVERT: C 1019 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7776 (tmm160) REVERT: D 64 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6710 (t80) REVERT: D 146 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6274 (tp) REVERT: D 172 HIS cc_start: 0.7812 (m-70) cc_final: 0.7593 (m-70) REVERT: E 17 GLU cc_start: 0.6831 (pm20) cc_final: 0.6410 (pm20) REVERT: E 54 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8535 (tmm-80) REVERT: E 62 PHE cc_start: 0.5729 (m-10) cc_final: 0.5259 (m-10) REVERT: E 75 ILE cc_start: 0.5270 (mm) cc_final: 0.5046 (mm) REVERT: E 92 SER cc_start: 0.7412 (t) cc_final: 0.7157 (m) REVERT: E 142 ARG cc_start: 0.7779 (tpt90) cc_final: 0.7557 (tmm160) REVERT: E 179 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7415 (mp) REVERT: E 183 LYS cc_start: 0.8950 (ptmm) cc_final: 0.8620 (ptpp) REVERT: E 195 GLU cc_start: 0.7331 (tt0) cc_final: 0.6527 (tp30) REVERT: G 10 GLU cc_start: 0.7732 (tp30) cc_final: 0.6946 (tm-30) REVERT: G 52 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7951 (mm) REVERT: G 130 PHE cc_start: 0.7590 (m-80) cc_final: 0.7298 (m-10) REVERT: G 222 LYS cc_start: 0.6337 (OUTLIER) cc_final: 0.5995 (mptt) REVERT: H 20 THR cc_start: 0.8881 (m) cc_final: 0.8566 (p) REVERT: H 185 ASP cc_start: 0.6968 (t70) cc_final: 0.6665 (t70) REVERT: H 188 LYS cc_start: 0.8931 (pptt) cc_final: 0.8678 (pptt) REVERT: H 189 HIS cc_start: 0.6970 (m170) cc_final: 0.6519 (m-70) REVERT: J 32 TYR cc_start: 0.5762 (m-80) cc_final: 0.5433 (m-80) REVERT: J 80 TYR cc_start: 0.7528 (m-80) cc_final: 0.7244 (m-80) REVERT: J 87 ARG cc_start: 0.7529 (mtm110) cc_final: 0.6961 (mpt180) REVERT: K 4 LEU cc_start: 0.6622 (mp) cc_final: 0.6353 (mt) REVERT: K 39 LYS cc_start: 0.8460 (mmmt) cc_final: 0.8179 (mmmt) REVERT: K 82 ASP cc_start: 0.5907 (OUTLIER) cc_final: 0.5106 (t0) REVERT: K 149 LYS cc_start: 0.6636 (mmtt) cc_final: 0.6170 (mmmt) REVERT: K 169 LYS cc_start: 0.8131 (mppt) cc_final: 0.7678 (mmtm) outliers start: 269 outliers final: 87 residues processed: 913 average time/residue: 0.5239 time to fit residues: 601.5884 Evaluate side-chains 642 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 534 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain A residue 140 PHE 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 267 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL 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 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 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 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 46 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 67 ARG 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 186 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 4 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 371 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 338 optimal weight: 0.9990 chunk 210 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 363 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 755 GLN A 784 GLN A 914 ASN A 954 GLN B 52 GLN B 207 HIS B 394 ASN B 414 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 787 GLN B 804 GLN B 901 GLN B 926 GLN B 935 GLN C 239 GLN C 388 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 166 GLN G 31 ASN G 43 GLN H 53 ASN H 89 GLN J 163 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.142373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.123497 restraints weight = 101176.671| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.64 r_work: 0.3638 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 1.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35056 Z= 0.160 Angle : 0.831 15.420 47794 Z= 0.402 Chirality : 0.051 0.745 5561 Planarity : 0.005 0.076 6072 Dihedral : 4.986 31.351 4625 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.91 % Favored : 94.07 % Rotamer: Outliers : 4.67 % Allowed : 28.42 % Favored : 66.92 % 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: -1.79 (0.12), residues: 4265 helix: 0.69 (0.20), residues: 683 sheet: -0.76 (0.14), residues: 1284 loop : -2.10 (0.12), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 319 TYR 0.024 0.002 TYR A 380 PHE 0.038 0.002 PHE A 562 TRP 0.027 0.002 TRP J 47 HIS 0.013 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (34951) covalent geometry : angle 0.80875 / 0.40 (47530) SS BOND : bond 0.00530 / 0.31 ( 51) SS BOND : angle 2.64045 / 1.68 ( 102) hydrogen bonds : bond 0.04604 / 3.01 ( 1137) hydrogen bonds : angle 5.84766 / 4.02 ( 3228) link_BETA1-4 : bond 0.00696 / 0.46 ( 17) link_BETA1-4 : angle 2.10940 / 1.51 ( 51) link_NAG-ASN : bond 0.00416 / 0.24 ( 37) link_NAG-ASN : angle 2.98322 / 2.21 ( 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 760 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 585 time to evaluate : 1.277 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: A 153 MET cc_start: 0.1377 (mmp) cc_final: 0.0289 (ptp) REVERT: A 203 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7932 (mm) REVERT: A 275 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6190 (t80) REVERT: A 305 SER cc_start: 0.8942 (t) cc_final: 0.8633 (p) REVERT: A 561 PRO cc_start: 0.8246 (Cg_exo) cc_final: 0.8039 (Cg_endo) REVERT: A 722 VAL cc_start: 0.8584 (m) cc_final: 0.8336 (t) REVERT: A 869 MET cc_start: 0.8992 (mpt) cc_final: 0.8035 (mtm) REVERT: A 878 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8784 (tt) REVERT: A 884 SER cc_start: 0.8660 (m) cc_final: 0.8393 (t) REVERT: B 135 PHE cc_start: 0.4440 (OUTLIER) cc_final: 0.3754 (p90) REVERT: B 138 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6669 (p0) REVERT: B 470 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7742 (p) REVERT: B 508 TYR cc_start: 0.5769 (OUTLIER) cc_final: 0.4814 (m-10) REVERT: B 697 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8351 (ttm) REVERT: B 710 ASN cc_start: 0.7265 (t0) cc_final: 0.6962 (t0) REVERT: B 762 GLN cc_start: 0.8164 (mm110) cc_final: 0.7865 (mm-40) REVERT: B 995 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7667 (mtp85) REVERT: C 153 MET cc_start: 0.3399 (ptm) cc_final: 0.2693 (ptt) REVERT: C 306 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.7090 (m-10) REVERT: C 314 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8450 (mt0) REVERT: C 329 PHE cc_start: 0.6671 (m-80) cc_final: 0.5098 (p90) REVERT: C 508 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.6131 (t80) REVERT: C 525 CYS cc_start: 0.4076 (OUTLIER) cc_final: 0.3856 (t) REVERT: C 663 ASP cc_start: 0.6612 (t70) cc_final: 0.6172 (t0) REVERT: C 664 ILE cc_start: 0.7847 (tp) cc_final: 0.7469 (mt) REVERT: C 756 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7582 (t80) REVERT: C 773 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8031 (tt0) REVERT: C 873 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.6088 (t80) REVERT: C 900 MET cc_start: 0.9070 (mtm) cc_final: 0.8767 (mtm) REVERT: C 1019 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8134 (tmm160) REVERT: D 172 HIS cc_start: 0.7932 (m-70) cc_final: 0.7713 (m-70) REVERT: D 197 LEU cc_start: 0.8882 (mm) cc_final: 0.8593 (pp) REVERT: D 207 ASN cc_start: 0.8177 (t0) cc_final: 0.7644 (m-40) REVERT: E 39 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6467 (mtmm) REVERT: E 54 ARG cc_start: 0.8819 (ttp80) cc_final: 0.8607 (tmm-80) REVERT: E 75 ILE cc_start: 0.6070 (mm) cc_final: 0.5677 (mm) REVERT: E 82 ASP cc_start: 0.7894 (m-30) cc_final: 0.7139 (m-30) REVERT: E 92 SER cc_start: 0.7671 (t) cc_final: 0.7445 (m) REVERT: E 158 ASN cc_start: 0.6729 (t0) cc_final: 0.6510 (t160) REVERT: G 222 LYS cc_start: 0.6300 (OUTLIER) cc_final: 0.5941 (mptt) REVERT: H 20 THR cc_start: 0.8863 (m) cc_final: 0.8613 (p) REVERT: H 185 ASP cc_start: 0.6725 (t70) cc_final: 0.6434 (t0) REVERT: H 188 LYS cc_start: 0.8930 (pptt) cc_final: 0.8656 (pptt) REVERT: J 46 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6504 (pm20) REVERT: J 67 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7779 (mtm180) REVERT: J 87 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7025 (mpt180) REVERT: K 4 LEU cc_start: 0.6805 (mp) cc_final: 0.6515 (mt) REVERT: K 82 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5675 (t0) REVERT: K 133 VAL cc_start: 0.8469 (p) cc_final: 0.8102 (t) REVERT: K 169 LYS cc_start: 0.8202 (mppt) cc_final: 0.7763 (mmtm) outliers start: 175 outliers final: 70 residues processed: 698 average time/residue: 0.5025 time to fit residues: 442.2334 Evaluate side-chains 588 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 498 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU 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 1068 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1130 ILE 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 301 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 167 LEU 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 107 LYS Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 186 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 384 optimal weight: 2.9990 chunk 265 optimal weight: 0.8980 chunk 399 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 233 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1005 GLN B1142 GLN C 388 ASN ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN K 210 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.139515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.119352 restraints weight = 100444.549| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.70 r_work: 0.3548 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 1.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 35056 Z= 0.211 Angle : 0.887 14.393 47794 Z= 0.435 Chirality : 0.052 0.389 5561 Planarity : 0.006 0.090 6072 Dihedral : 5.108 29.660 4625 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.53 % Favored : 92.40 % Rotamer: Outliers : 4.75 % Allowed : 29.30 % Favored : 65.96 % Cbeta Deviations : 0.02 % 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: -1.75 (0.12), residues: 4265 helix: 0.66 (0.20), residues: 681 sheet: -0.76 (0.14), residues: 1268 loop : -2.01 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 61 TYR 0.034 0.002 TYR H 140 PHE 0.075 0.002 PHE A 140 TRP 0.031 0.003 TRP K 148 HIS 0.014 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (34951) covalent geometry : angle 0.86850 / 0.43 (47530) SS BOND : bond 0.00531 / 0.34 ( 51) SS BOND : angle 2.41850 / 1.56 ( 102) hydrogen bonds : bond 0.04843 / 3.19 ( 1137) hydrogen bonds : angle 5.77755 / 3.99 ( 3228) link_BETA1-4 : bond 0.00598 / 0.41 ( 17) link_BETA1-4 : angle 1.75606 / 1.06 ( 51) link_NAG-ASN : bond 0.00666 / 0.43 ( 37) link_NAG-ASN : angle 3.01156 / 2.19 ( 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 734 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 556 time to evaluate : 1.443 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 114 THR cc_start: 0.4796 (OUTLIER) cc_final: 0.4270 (p) REVERT: A 153 MET cc_start: 0.0868 (mmp) cc_final: 0.0127 (pmt) REVERT: A 203 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8311 (mm) REVERT: A 421 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6790 (p90) REVERT: A 428 ASP cc_start: 0.7781 (t0) cc_final: 0.7404 (p0) REVERT: A 516 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6505 (tm-30) REVERT: A 722 VAL cc_start: 0.8862 (m) cc_final: 0.8590 (t) REVERT: A 755 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7616 (tp-100) REVERT: A 894 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8262 (mp) REVERT: B 135 PHE cc_start: 0.4684 (OUTLIER) cc_final: 0.4028 (p90) REVERT: B 138 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6833 (p0) REVERT: B 170 TYR cc_start: 0.4528 (OUTLIER) cc_final: 0.4244 (t80) REVERT: B 470 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7978 (p) REVERT: B 576 VAL cc_start: 0.8547 (t) cc_final: 0.8290 (t) REVERT: B 697 MET cc_start: 0.8785 (ttt) cc_final: 0.8566 (ttm) REVERT: B 710 ASN cc_start: 0.8019 (t0) cc_final: 0.7723 (t0) REVERT: B 731 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8655 (ptp) REVERT: B 995 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.8048 (mtp85) REVERT: C 92 PHE cc_start: 0.7823 (t80) cc_final: 0.7469 (m-80) REVERT: C 153 MET cc_start: 0.3554 (ptm) cc_final: 0.2871 (ptt) REVERT: C 223 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6941 (pp) REVERT: C 226 LEU cc_start: 0.7468 (tp) cc_final: 0.7215 (tm) REVERT: C 267 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7627 (t) REVERT: C 552 LEU cc_start: 0.8973 (tm) cc_final: 0.8733 (mm) REVERT: C 661 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6530 (tp30) REVERT: C 664 ILE cc_start: 0.8042 (tp) cc_final: 0.7823 (mt) REVERT: C 756 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.7918 (t80) REVERT: C 873 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.6212 (t80) REVERT: C 993 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8695 (mt) REVERT: C 1019 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8241 (tmm160) REVERT: D 152 ASP cc_start: 0.8800 (t0) cc_final: 0.8554 (m-30) REVERT: D 197 LEU cc_start: 0.9019 (mm) cc_final: 0.8714 (pp) REVERT: D 207 ASN cc_start: 0.8426 (t0) cc_final: 0.7925 (m-40) REVERT: E 33 LEU cc_start: 0.8652 (mt) cc_final: 0.8439 (tp) REVERT: E 39 LYS cc_start: 0.7385 (ptpp) cc_final: 0.7106 (mtmm) REVERT: E 42 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7404 (tp40) REVERT: E 54 ARG cc_start: 0.9008 (ttp80) cc_final: 0.8741 (tmm-80) REVERT: E 62 PHE cc_start: 0.6315 (m-10) cc_final: 0.5842 (m-10) REVERT: E 75 ILE cc_start: 0.6516 (mm) cc_final: 0.6155 (mm) REVERT: E 82 ASP cc_start: 0.8572 (m-30) cc_final: 0.7805 (m-30) REVERT: E 92 SER cc_start: 0.8022 (t) cc_final: 0.7659 (m) REVERT: E 183 LYS cc_start: 0.9107 (ptmm) cc_final: 0.8887 (ptmt) REVERT: E 195 GLU cc_start: 0.7755 (tt0) cc_final: 0.6970 (tp30) REVERT: G 10 GLU cc_start: 0.7702 (tp30) cc_final: 0.7421 (tm-30) REVERT: G 73 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7371 (p0) REVERT: G 179 GLN cc_start: 0.9006 (mp10) cc_final: 0.8799 (mp10) REVERT: G 222 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6225 (mptt) REVERT: H 17 GLU cc_start: 0.7669 (mp0) cc_final: 0.7242 (mp0) REVERT: J 32 TYR cc_start: 0.5403 (m-80) cc_final: 0.5166 (m-80) REVERT: J 48 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8188 (ttm) REVERT: J 64 PHE cc_start: 0.8409 (m-80) cc_final: 0.8122 (m-80) REVERT: K 47 LEU cc_start: 0.7559 (mt) cc_final: 0.7277 (mm) REVERT: K 170 ASP cc_start: 0.8480 (t0) cc_final: 0.7838 (t0) outliers start: 178 outliers final: 76 residues processed: 676 average time/residue: 0.5714 time to fit residues: 480.5722 Evaluate side-chains 547 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 453 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 894 LEU 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 1068 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE 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 170 TYR Chi-restraints excluded: chain B residue 301 CYS 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 421 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 140 SER 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 132 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 186 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 10 optimal weight: 0.0980 chunk 130 optimal weight: 2.9990 chunk 298 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 368 optimal weight: 1.9990 chunk 329 optimal weight: 3.9990 chunk 142 optimal weight: 0.0270 chunk 94 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 914 ASN A 957 GLN A1005 GLN B 207 HIS B 422 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 409 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN E 158 ASN G 31 ASN H 53 ASN H 89 GLN J 163 ASN K 147 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.116333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.091413 restraints weight = 89129.881| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.39 r_work: 0.3490 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 1.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35056 Z= 0.153 Angle : 0.832 12.541 47794 Z= 0.403 Chirality : 0.049 0.386 5561 Planarity : 0.005 0.075 6072 Dihedral : 4.898 28.952 4625 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.31 % Favored : 93.67 % Rotamer: Outliers : 3.63 % Allowed : 31.94 % Favored : 64.43 % 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 (0.13), residues: 4265 helix: 0.90 (0.21), residues: 674 sheet: -0.54 (0.14), residues: 1262 loop : -1.99 (0.12), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 408 TYR 0.025 0.001 TYR H 140 PHE 0.033 0.002 PHE A 562 TRP 0.053 0.002 TRP D 162 HIS 0.012 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (34951) covalent geometry : angle 0.81638 / 0.40 (47530) SS BOND : bond 0.00447 / 0.29 ( 51) SS BOND : angle 2.30942 / 1.48 ( 102) hydrogen bonds : bond 0.04272 / 2.77 ( 1137) hydrogen bonds : angle 5.56910 / 3.83 ( 3228) link_BETA1-4 : bond 0.00610 / 0.40 ( 17) link_BETA1-4 : angle 1.61860 / 0.98 ( 51) link_NAG-ASN : bond 0.00467 / 0.28 ( 37) link_NAG-ASN : angle 2.60074 / 1.94 ( 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 622 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 486 time to evaluate : 1.432 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 114 THR cc_start: 0.4609 (OUTLIER) cc_final: 0.4075 (p) REVERT: A 153 MET cc_start: 0.0928 (mmp) cc_final: 0.0044 (pmt) REVERT: A 421 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6707 (p90) REVERT: A 428 ASP cc_start: 0.7761 (t0) cc_final: 0.7302 (p0) REVERT: A 462 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8276 (ptpp) REVERT: A 516 GLU cc_start: 0.6406 (tm-30) cc_final: 0.6163 (tm-30) REVERT: A 661 GLU cc_start: 0.7889 (mp0) cc_final: 0.7686 (mm-30) REVERT: A 755 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7531 (tp-100) REVERT: A 1005 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8313 (tp40) REVERT: A 1096 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.9046 (t) REVERT: A 1117 THR cc_start: 0.7808 (m) cc_final: 0.7591 (p) REVERT: B 84 LEU cc_start: 0.6292 (tp) cc_final: 0.5707 (mt) REVERT: B 135 PHE cc_start: 0.4695 (OUTLIER) cc_final: 0.4020 (p90) REVERT: B 138 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6865 (p0) REVERT: B 170 TYR cc_start: 0.4583 (OUTLIER) cc_final: 0.4329 (t80) REVERT: B 470 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7984 (p) REVERT: B 697 MET cc_start: 0.8692 (ttt) cc_final: 0.8475 (ttm) REVERT: B 710 ASN cc_start: 0.7835 (t0) cc_final: 0.7547 (t0) REVERT: B 882 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8706 (mt) REVERT: B 933 LYS cc_start: 0.8330 (mmpt) cc_final: 0.8071 (mmmm) REVERT: C 153 MET cc_start: 0.3510 (ptm) cc_final: 0.2874 (ptt) REVERT: C 192 PHE cc_start: 0.7534 (m-80) cc_final: 0.7233 (m-80) REVERT: C 226 LEU cc_start: 0.7592 (tp) cc_final: 0.7285 (tm) REVERT: C 309 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7617 (pp20) REVERT: C 415 THR cc_start: 0.6723 (OUTLIER) cc_final: 0.5268 (p) REVERT: C 473 TYR cc_start: 0.7486 (t80) cc_final: 0.7142 (t80) REVERT: C 508 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6074 (t80) REVERT: C 552 LEU cc_start: 0.9098 (tm) cc_final: 0.8806 (mm) REVERT: C 756 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: C 873 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.5989 (t80) REVERT: C 1019 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8148 (tmm160) REVERT: C 1115 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8087 (mt) REVERT: D 73 ASP cc_start: 0.6677 (t70) cc_final: 0.6474 (t0) REVERT: D 81 MET cc_start: 0.8418 (tpp) cc_final: 0.7951 (tpp) REVERT: D 152 ASP cc_start: 0.8740 (t0) cc_final: 0.8398 (m-30) REVERT: D 197 LEU cc_start: 0.9033 (mm) cc_final: 0.8702 (pp) REVERT: D 207 ASN cc_start: 0.8506 (t0) cc_final: 0.8004 (m-40) REVERT: E 62 PHE cc_start: 0.6506 (m-10) cc_final: 0.6198 (m-10) REVERT: E 75 ILE cc_start: 0.6893 (mm) cc_final: 0.6542 (mm) REVERT: E 82 ASP cc_start: 0.8477 (m-30) cc_final: 0.7773 (m-30) REVERT: E 92 SER cc_start: 0.7992 (t) cc_final: 0.7635 (m) REVERT: E 183 LYS cc_start: 0.9125 (ptmm) cc_final: 0.8898 (ptpp) REVERT: G 10 GLU cc_start: 0.7622 (tp30) cc_final: 0.7247 (tm-30) REVERT: G 222 LYS cc_start: 0.6366 (OUTLIER) cc_final: 0.6016 (mptt) REVERT: H 17 GLU cc_start: 0.7614 (mp0) cc_final: 0.7270 (mp0) REVERT: K 45 ARG cc_start: 0.9162 (ppt-90) cc_final: 0.8956 (ppt-90) REVERT: K 47 LEU cc_start: 0.7938 (mt) cc_final: 0.7585 (mm) outliers start: 136 outliers final: 69 residues processed: 581 average time/residue: 0.5073 time to fit residues: 370.4752 Evaluate side-chains 521 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 436 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE 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 170 TYR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 882 ILE 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 160 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 91 THR 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 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 160 VAL Chi-restraints excluded: chain J residue 186 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 58 ILE Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 83 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 316 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 389 optimal weight: 0.9990 chunk 348 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 226 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 422 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1106 GLN B 207 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 710 ASN ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 163 ASN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN G 31 ASN G 59 ASN H 53 ASN ** H 155 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 = 0.4002 r_free = 0.4002 target = 0.114082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.088636 restraints weight = 88807.513| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.39 r_work: 0.3436 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 1.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 35056 Z= 0.185 Angle : 0.863 14.393 47794 Z= 0.421 Chirality : 0.051 0.452 5561 Planarity : 0.005 0.077 6072 Dihedral : 4.972 27.101 4625 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.43 % Favored : 92.50 % Rotamer: Outliers : 3.36 % Allowed : 32.63 % Favored : 64.01 % 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 (0.13), residues: 4265 helix: 0.86 (0.21), residues: 669 sheet: -0.62 (0.14), residues: 1300 loop : -1.93 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 319 TYR 0.024 0.002 TYR A 473 PHE 0.034 0.002 PHE B 562 TRP 0.038 0.002 TRP K 148 HIS 0.011 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (34951) covalent geometry : angle 0.84825 / 0.42 (47530) SS BOND : bond 0.00725 / 0.37 ( 51) SS BOND : angle 2.29471 / 1.48 ( 102) hydrogen bonds : bond 0.04573 / 3.01 ( 1137) hydrogen bonds : angle 5.57536 / 3.82 ( 3228) link_BETA1-4 : bond 0.00549 / 0.36 ( 17) link_BETA1-4 : angle 1.62913 / 0.98 ( 51) link_NAG-ASN : bond 0.00454 / 0.28 ( 37) link_NAG-ASN : angle 2.61662 / 1.96 ( 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 609 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 483 time to evaluate : 1.326 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: 0.0658 (mmp) cc_final: -0.0104 (pmt) REVERT: A 408 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7981 (ptm-80) REVERT: A 421 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6361 (p90) REVERT: A 428 ASP cc_start: 0.8097 (t0) cc_final: 0.7544 (p0) REVERT: A 516 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6391 (tm-30) REVERT: A 697 MET cc_start: 0.7755 (tpp) cc_final: 0.7443 (mmt) REVERT: A 1117 THR cc_start: 0.7862 (m) cc_final: 0.7648 (p) REVERT: A 1129 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8913 (t) REVERT: B 84 LEU cc_start: 0.6413 (tp) cc_final: 0.6123 (mt) REVERT: B 135 PHE cc_start: 0.4771 (OUTLIER) cc_final: 0.4021 (p90) REVERT: B 138 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6994 (p0) REVERT: B 170 TYR cc_start: 0.4916 (OUTLIER) cc_final: 0.4702 (t80) REVERT: B 470 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8162 (p) REVERT: B 710 ASN cc_start: 0.8156 (t0) cc_final: 0.7901 (t0) REVERT: B 994 ASP cc_start: 0.8559 (m-30) cc_final: 0.7945 (t0) REVERT: C 104 TRP cc_start: 0.7029 (m-90) cc_final: 0.6741 (m-90) REVERT: C 153 MET cc_start: 0.3736 (ptm) cc_final: 0.3084 (ptt) REVERT: C 226 LEU cc_start: 0.8013 (tp) cc_final: 0.7788 (tm) REVERT: C 309 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 473 TYR cc_start: 0.7559 (t80) cc_final: 0.7307 (t80) REVERT: C 508 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6770 (t80) REVERT: C 552 LEU cc_start: 0.9160 (tm) cc_final: 0.8948 (mm) REVERT: C 873 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.6059 (t80) REVERT: C 1019 ARG cc_start: 0.8749 (ppp80) cc_final: 0.8193 (tmm160) REVERT: C 1115 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8063 (mt) REVERT: D 50 ARG cc_start: 0.8718 (ptm-80) cc_final: 0.8511 (ttt-90) REVERT: D 81 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7592 (tpp) REVERT: D 146 LEU cc_start: 0.8524 (tt) cc_final: 0.7871 (tp) REVERT: D 152 ASP cc_start: 0.8791 (t0) cc_final: 0.8492 (m-30) REVERT: D 179 GLN cc_start: 0.7681 (pt0) cc_final: 0.7359 (mp10) REVERT: D 197 LEU cc_start: 0.8968 (mm) cc_final: 0.8670 (pp) REVERT: D 207 ASN cc_start: 0.8494 (t0) cc_final: 0.8097 (m-40) REVERT: E 10 THR cc_start: 0.7849 (p) cc_final: 0.7629 (t) REVERT: E 54 ARG cc_start: 0.8896 (tmm-80) cc_final: 0.8629 (tmm-80) REVERT: E 75 ILE cc_start: 0.7597 (mm) cc_final: 0.7391 (mm) REVERT: E 82 ASP cc_start: 0.8448 (m-30) cc_final: 0.7882 (m-30) REVERT: E 195 GLU cc_start: 0.8036 (tt0) cc_final: 0.7822 (pp20) REVERT: G 2 VAL cc_start: 0.7690 (t) cc_final: 0.7426 (m) REVERT: G 10 GLU cc_start: 0.7886 (tp30) cc_final: 0.6978 (tm-30) REVERT: G 222 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6140 (mptt) REVERT: H 17 GLU cc_start: 0.7750 (mp0) cc_final: 0.7107 (mp0) REVERT: H 161 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8273 (tp30) REVERT: H 188 LYS cc_start: 0.8955 (pptt) cc_final: 0.8518 (pptt) REVERT: J 32 TYR cc_start: 0.5488 (m-80) cc_final: 0.5196 (m-80) REVERT: J 84 ARG cc_start: 0.7682 (pmt170) cc_final: 0.7433 (pmt170) REVERT: K 10 THR cc_start: 0.7902 (p) cc_final: 0.7677 (t) REVERT: K 47 LEU cc_start: 0.7966 (mt) cc_final: 0.7616 (mm) REVERT: K 195 GLU cc_start: 0.7340 (tp30) cc_final: 0.6585 (pp20) outliers start: 126 outliers final: 68 residues processed: 573 average time/residue: 0.5496 time to fit residues: 395.8570 Evaluate side-chains 505 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 426 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1129 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 135 PHE 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 301 CYS Chi-restraints excluded: chain B residue 302 THR 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 421 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 91 THR 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 56 THR 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 160 VAL Chi-restraints excluded: chain J residue 186 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 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 39 optimal weight: 3.9990 chunk 412 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 224 optimal weight: 0.9980 chunk 347 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 405 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 360 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 755 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1106 GLN B 49 HIS B 207 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN D 6 GLN D 163 ASN G 31 ASN G 113 GLN H 53 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.113462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.087995 restraints weight = 89014.590| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.37 r_work: 0.3424 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 1.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35056 Z= 0.177 Angle : 0.872 14.703 47794 Z= 0.423 Chirality : 0.051 0.471 5561 Planarity : 0.005 0.084 6072 Dihedral : 4.987 30.009 4625 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.57 % Favored : 93.41 % Rotamer: Outliers : 2.83 % Allowed : 33.56 % Favored : 63.61 % 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: -1.46 (0.13), residues: 4265 helix: 0.94 (0.21), residues: 654 sheet: -0.45 (0.14), residues: 1260 loop : -1.89 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 319 TYR 0.035 0.002 TYR E 140 PHE 0.044 0.002 PHE A 562 TRP 0.029 0.002 TRP D 162 HIS 0.013 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (34951) covalent geometry : angle 0.85632 / 0.42 (47530) SS BOND : bond 0.00475 / 0.30 ( 51) SS BOND : angle 2.24178 / 1.47 ( 102) hydrogen bonds : bond 0.04374 / 2.87 ( 1137) hydrogen bonds : angle 5.58321 / 3.84 ( 3228) link_BETA1-4 : bond 0.00637 / 0.38 ( 17) link_BETA1-4 : angle 1.65296 / 1.03 ( 51) link_NAG-ASN : bond 0.00521 / 0.32 ( 37) link_NAG-ASN : angle 2.70508 / 2.04 ( 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 574 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 468 time to evaluate : 1.264 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: 0.0658 (mmp) cc_final: -0.0038 (pmt) REVERT: A 275 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7360 (t80) REVERT: A 421 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6171 (p90) REVERT: A 516 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6398 (tm-30) REVERT: A 1010 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8810 (mm110) REVERT: B 135 PHE cc_start: 0.4869 (OUTLIER) cc_final: 0.4115 (p90) REVERT: B 138 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7125 (p0) REVERT: B 170 TYR cc_start: 0.5180 (OUTLIER) cc_final: 0.4900 (t80) REVERT: B 237 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.6674 (mtm-85) REVERT: B 312 ILE cc_start: 0.8994 (mm) cc_final: 0.8661 (tp) REVERT: B 418 ILE cc_start: 0.8882 (tp) cc_final: 0.8615 (mp) REVERT: B 470 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 710 ASN cc_start: 0.7995 (t0) cc_final: 0.7794 (t0) REVERT: B 994 ASP cc_start: 0.8577 (m-30) cc_final: 0.8021 (t0) REVERT: C 153 MET cc_start: 0.3434 (ptm) cc_final: 0.2941 (ptt) REVERT: C 169 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6953 (tp30) REVERT: C 309 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 508 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.6666 (t80) REVERT: C 599 THR cc_start: 0.8899 (p) cc_final: 0.8674 (p) REVERT: C 710 ASN cc_start: 0.8318 (m-40) cc_final: 0.7906 (p0) REVERT: C 873 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6115 (t80) REVERT: C 1002 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8317 (tp-100) REVERT: C 1019 ARG cc_start: 0.8729 (ppp80) cc_final: 0.8185 (tmm160) REVERT: C 1115 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8255 (mt) REVERT: D 81 MET cc_start: 0.8479 (tpp) cc_final: 0.7825 (tpp) REVERT: D 146 LEU cc_start: 0.8736 (tt) cc_final: 0.8149 (tp) REVERT: D 152 ASP cc_start: 0.8664 (t0) cc_final: 0.8460 (m-30) REVERT: D 179 GLN cc_start: 0.7735 (pt0) cc_final: 0.7482 (mp10) REVERT: D 197 LEU cc_start: 0.9006 (mm) cc_final: 0.8724 (pp) REVERT: D 207 ASN cc_start: 0.8498 (t0) cc_final: 0.8184 (m-40) REVERT: E 70 ASP cc_start: 0.8757 (m-30) cc_final: 0.8519 (t70) REVERT: E 75 ILE cc_start: 0.7920 (mm) cc_final: 0.7640 (mm) REVERT: E 82 ASP cc_start: 0.8458 (m-30) cc_final: 0.8154 (m-30) REVERT: E 103 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8207 (tmtt) REVERT: E 132 VAL cc_start: 0.8853 (m) cc_final: 0.8624 (t) REVERT: E 145 LYS cc_start: 0.7403 (tppt) cc_final: 0.6857 (ttpp) REVERT: G 2 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7508 (m) REVERT: G 3 GLN cc_start: 0.8357 (mp10) cc_final: 0.8142 (mm110) REVERT: G 10 GLU cc_start: 0.7910 (tp30) cc_final: 0.7509 (tm-30) REVERT: G 203 ILE cc_start: 0.9044 (pp) cc_final: 0.8372 (mm) REVERT: G 222 LYS cc_start: 0.6539 (OUTLIER) cc_final: 0.6221 (mptt) REVERT: H 10 THR cc_start: 0.8466 (t) cc_final: 0.8258 (t) REVERT: H 103 LYS cc_start: 0.8485 (tptt) cc_final: 0.8145 (tptt) REVERT: H 147 GLN cc_start: 0.8887 (mt0) cc_final: 0.8578 (mm110) REVERT: H 185 ASP cc_start: 0.7792 (p0) cc_final: 0.7577 (p0) REVERT: H 188 LYS cc_start: 0.9008 (pptt) cc_final: 0.8770 (pptt) REVERT: J 32 TYR cc_start: 0.5325 (m-80) cc_final: 0.5050 (m-80) REVERT: K 10 THR cc_start: 0.8106 (p) cc_final: 0.7840 (t) REVERT: K 18 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7358 (mmm160) REVERT: K 123 GLU cc_start: 0.9076 (tp30) cc_final: 0.8102 (pp20) outliers start: 106 outliers final: 61 residues processed: 548 average time/residue: 0.5099 time to fit residues: 352.6052 Evaluate side-chains 501 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 426 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 126 VAL 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 170 TYR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR 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 160 TYR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain G residue 2 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 191 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 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 160 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 98 optimal weight: 0.0020 chunk 410 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 414 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 364 optimal weight: 3.9990 chunk 372 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 360 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 207 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1142 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN E 158 ASN G 31 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN J 163 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.116090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.088928 restraints weight = 92621.324| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 4.08 r_work: 0.3366 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 1.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 35056 Z= 0.196 Angle : 0.880 13.931 47794 Z= 0.430 Chirality : 0.051 0.511 5561 Planarity : 0.005 0.078 6072 Dihedral : 5.064 28.994 4625 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.39 % Favored : 92.59 % Rotamer: Outliers : 2.72 % Allowed : 34.12 % Favored : 63.15 % 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: -1.50 (0.13), residues: 4265 helix: 0.91 (0.21), residues: 656 sheet: -0.55 (0.14), residues: 1275 loop : -1.87 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 87 TYR 0.040 0.002 TYR J 94 PHE 0.028 0.002 PHE B 562 TRP 0.043 0.002 TRP K 148 HIS 0.012 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (34951) covalent geometry : angle 0.86129 / 0.42 (47530) SS BOND : bond 0.00649 / 0.38 ( 51) SS BOND : angle 2.82331 / 1.78 ( 102) hydrogen bonds : bond 0.04591 / 3.02 ( 1137) hydrogen bonds : angle 5.61927 / 3.84 ( 3228) link_BETA1-4 : bond 0.00483 / 0.32 ( 17) link_BETA1-4 : angle 1.68465 / 1.01 ( 51) link_NAG-ASN : bond 0.00449 / 0.27 ( 37) link_NAG-ASN : angle 2.74124 / 2.06 ( 111) =============================================================================== Job complete usr+sys time: 17792.64 seconds wall clock time: 302 minutes 41.79 seconds (18161.79 seconds total)