Starting phenix.real_space_refine on Sun Jun 29 13:09:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whb_32498/06_2025/7whb_32498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whb_32498/06_2025/7whb_32498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whb_32498/06_2025/7whb_32498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whb_32498/06_2025/7whb_32498.map" model { file = "/net/cci-nas-00/data/ceres_data/7whb_32498/06_2025/7whb_32498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whb_32498/06_2025/7whb_32498.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 11 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34209 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "D" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "H" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "J" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "K" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 19.27, per 1000 atoms: 0.56 Number of scatterers: 34209 At special positions: 0 Unit cell: (166.881, 173.468, 248.125, 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=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.03 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, 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 a 1 " - " NAG a 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 603 " " NAG A1404 " - " ASN A 616 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " 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 C1201 " - " ASN A 282 " " NAG C1202 " - " ASN C 61 " " NAG C1203 " - " ASN C 122 " " NAG C1204 " - " ASN C 282 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 616 " " NAG C1207 " - " ASN C 657 " " 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 331 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 709 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.45 Conformation dependent library (CDL) restraints added in 4.2 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: 72 helices and 78 sheets defined 18.4% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.021A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 5.203A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.043A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.500A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.988A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.829A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.733A 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 976 through 982 Processing helix chain 'A' and resid 988 through 1033 removed outlier: 3.615A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.853A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (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 364 through 370 removed outlier: 4.037A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 5.108A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.511A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (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 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 939 removed outlier: 6.798A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.844A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.689A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.167A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.511A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.050A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 5.233A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.847A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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: 3.683A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.841A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.083A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.666A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.692A 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 984 removed outlier: 3.576A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.058A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.575A pdb=" N GLN D 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 164 through 166 No H-bonds generated for 'chain 'D' and resid 164 through 166' Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.952A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 197 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.938A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.902A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 197 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.942A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.670A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.198A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.854A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.556A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.690A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 539 removed outlier: 5.012A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.576A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.458A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.338A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.728A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.966A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 49 through 51 removed outlier: 6.864A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.507A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.539A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.009A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.094A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.628A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.685A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.685A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.009A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.620A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.553A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.561A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.811A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.050A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.944A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.704A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.875A 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: 6.704A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.602A 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 6 removed outlier: 3.872A 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: 3.505A pdb=" N ASN D 59 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.111A 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: 3.505A pdb=" N ASN D 59 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 94 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.670A pdb=" N LYS D 151 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER D 188 " --> pdb=" O CYS D 148 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.670A pdb=" N LYS D 151 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS D 151 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU D 186 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 161 through 162 removed outlier: 3.595A pdb=" N VAL D 215 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.509A pdb=" N ARG E 24 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS E 23 " --> pdb=" O PHE E 71 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.518A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.894A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 153 through 155 removed outlier: 4.577A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.952A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.917A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN G 59 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.164A pdb=" N VAL G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.715A pdb=" N LYS G 151 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER G 188 " --> pdb=" O CYS G 148 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.715A pdb=" N LYS G 151 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS G 151 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU G 186 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 158 through 162 removed outlier: 3.660A pdb=" N THR G 159 " --> pdb=" O ASN G 207 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS G 217 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL G 215 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS G 208 " --> pdb=" O THR G 213 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.705A pdb=" N SER H 7 " --> pdb=" O SER H 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS H 23 " --> pdb=" O PHE H 71 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.527A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.900A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.582A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.964A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.685A pdb=" N TYR J 94 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.685A pdb=" N TYR J 94 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL J 110 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 128 through 132 removed outlier: 3.558A pdb=" N LYS J 151 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER J 188 " --> pdb=" O CYS J 148 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 128 through 132 removed outlier: 3.558A pdb=" N LYS J 151 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS J 151 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU J 186 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 158 through 162 removed outlier: 3.764A pdb=" N THR J 159 " --> pdb=" O ASN J 207 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN J 207 " --> pdb=" O THR J 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS J 217 " --> pdb=" O CYS J 204 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL J 215 " --> pdb=" O VAL J 206 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.791A pdb=" N CYS K 23 " --> pdb=" O PHE K 71 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.541A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 114 through 118 removed outlier: 5.892A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.309A pdb=" N TRP K 148 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN K 147 " --> pdb=" O GLU K 195 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU K 195 " --> pdb=" O GLN K 147 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA K 193 " --> pdb=" O LYS K 149 " (cutoff:3.500A) 1313 hydrogen bonds defined for protein. 3426 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: 16.17 Time building geometry restraints manager: 10.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10928 1.35 - 1.47: 8827 1.47 - 1.59: 15013 1.59 - 1.72: 0 1.72 - 1.84: 183 Bond restraints: 34951 Sorted by residual: bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.93e+00 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C1 NAG C1203 " pdb=" O5 NAG C1203 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 34946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 46611 1.98 - 3.96: 838 3.96 - 5.94: 69 5.94 - 7.92: 8 7.92 - 9.90: 4 Bond angle restraints: 47530 Sorted by residual: angle pdb=" N ILE C 418 " pdb=" CA ILE C 418 " pdb=" C ILE C 418 " ideal model delta sigma weight residual 113.47 108.63 4.84 1.01e+00 9.80e-01 2.30e+01 angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 113.43 108.85 4.58 1.09e+00 8.42e-01 1.76e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.74 -5.04 1.22e+00 6.72e-01 1.71e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.68e+01 angle pdb=" N GLU C 281 " pdb=" CA GLU C 281 " pdb=" C GLU C 281 " ideal model delta sigma weight residual 114.75 109.99 4.76 1.26e+00 6.30e-01 1.43e+01 ... (remaining 47525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 19628 17.98 - 35.96: 1541 35.96 - 53.94: 285 53.94 - 71.92: 66 71.92 - 89.90: 63 Dihedral angle restraints: 21583 sinusoidal: 9051 harmonic: 12532 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -0.65 -85.35 1 1.00e+01 1.00e-02 8.82e+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 -5.04 -80.96 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -8.49 -77.51 1 1.00e+01 1.00e-02 7.52e+01 ... (remaining 21580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 5534 0.136 - 0.272: 26 0.272 - 0.409: 0 0.409 - 0.545: 0 0.545 - 0.681: 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 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG C1204 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1204 " pdb=" O5 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.99e-01 ... (remaining 5558 not shown) Planarity restraints: 6108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 986 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 156 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO G 157 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 157 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 157 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 983 " -0.127 9.50e-02 1.11e+02 5.72e-02 2.66e+00 pdb=" NE ARG B 983 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 983 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 983 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 983 " 0.000 2.00e-02 2.50e+03 ... (remaining 6105 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2232 2.73 - 3.28: 33511 3.28 - 3.82: 54324 3.82 - 4.36: 63317 4.36 - 4.90: 111731 Nonbonded interactions: 265115 Sorted by model distance: nonbonded pdb=" OH TYR C 674 " pdb=" N GLN C 690 " model vdw 2.193 3.120 nonbonded pdb=" NH1 ARG D 50 " pdb=" OE2 GLU D 99 " model vdw 2.200 3.120 nonbonded pdb=" CZ TYR C 674 " pdb=" N GLN C 690 " model vdw 2.220 3.340 nonbonded pdb=" O THR A 676 " pdb=" OG SER A 691 " model vdw 2.226 3.040 nonbonded pdb=" NH1 ARG J 50 " pdb=" OE2 GLU J 99 " model vdw 2.252 3.120 ... (remaining 265110 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 1146 or resid 1401 through 1405)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1405)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1146 or resid 1201 thr \ ough 1205)) } 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' selection = chain 'a' } 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: 2.690 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: 1.330 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 78.730 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.240 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: 0.000 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.003 0.043 35057 Z= 0.161 Angle : 0.621 15.654 47794 Z= 0.317 Chirality : 0.045 0.681 5561 Planarity : 0.004 0.057 6072 Dihedral : 13.908 89.897 13376 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.78 % Favored : 93.20 % Rotamer: Outliers : 0.27 % Allowed : 0.29 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4265 helix: 2.02 (0.21), residues: 674 sheet: -0.59 (0.15), residues: 1314 loop : -1.54 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.002 0.000 HIS A 49 PHE 0.019 0.001 PHE C 906 TYR 0.023 0.001 TYR E 49 ARG 0.014 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 36) link_NAG-ASN : angle 2.85948 ( 108) link_BETA1-4 : bond 0.00529 ( 18) link_BETA1-4 : angle 1.99962 ( 54) hydrogen bonds : bond 0.22865 ( 1237) hydrogen bonds : angle 8.74390 ( 3426) SS BOND : bond 0.00484 ( 51) SS BOND : angle 1.25073 ( 102) covalent geometry : bond 0.00333 (34951) covalent geometry : angle 0.60144 (47530) Misc. bond : bond 0.00011 ( 1) *********************** 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 326 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 316 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8691 (p90) cc_final: 0.8349 (p90) REVERT: A 340 GLU cc_start: 0.8295 (pt0) cc_final: 0.8086 (pp20) REVERT: A 773 GLU cc_start: 0.7878 (tt0) cc_final: 0.7658 (tt0) REVERT: B 269 TYR cc_start: 0.8579 (m-80) cc_final: 0.8317 (m-80) REVERT: B 651 ILE cc_start: 0.9275 (pt) cc_final: 0.9013 (pp) REVERT: B 776 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8505 (ttpt) REVERT: B 780 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7949 (mp0) REVERT: B 983 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8270 (mtm110) REVERT: B 1002 GLN cc_start: 0.8930 (tp40) cc_final: 0.8638 (tm-30) REVERT: B 1092 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7361 (pp20) REVERT: C 153 MET cc_start: 0.4122 (tpp) cc_final: 0.3600 (tpp) REVERT: C 780 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8079 (mp0) REVERT: C 814 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7513 (mmmt) REVERT: D 125 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8506 (tptp) REVERT: E 172 THR cc_start: 0.8626 (p) cc_final: 0.8282 (p) REVERT: E 210 ASN cc_start: 0.7705 (p0) cc_final: 0.7315 (p0) REVERT: H 210 ASN cc_start: 0.7779 (p0) cc_final: 0.7523 (p0) REVERT: K 210 ASN cc_start: 0.7932 (p0) cc_final: 0.7631 (p0) outliers start: 10 outliers final: 8 residues processed: 326 average time/residue: 1.2019 time to fit residues: 487.2115 Evaluate side-chains 248 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 238 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 128 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 6.9990 chunk 325 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 336 optimal weight: 5.9990 chunk 130 optimal weight: 0.0030 chunk 204 optimal weight: 6.9990 chunk 250 optimal weight: 0.7980 chunk 389 optimal weight: 0.9980 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 343 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 343 ASN C 388 ASN C1005 GLN E 138 ASN E 166 GLN H 27 GLN H 138 ASN H 166 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.092631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.068500 restraints weight = 98746.451| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.84 r_work: 0.3099 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 35057 Z= 0.207 Angle : 0.663 13.098 47794 Z= 0.331 Chirality : 0.046 0.480 5561 Planarity : 0.004 0.050 6072 Dihedral : 7.360 109.185 5777 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.25 % Favored : 92.73 % Rotamer: Outliers : 0.61 % Allowed : 7.95 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 4265 helix: 2.04 (0.21), residues: 680 sheet: -0.46 (0.14), residues: 1299 loop : -1.52 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 104 HIS 0.003 0.001 HIS J 208 PHE 0.016 0.001 PHE A 86 TYR 0.022 0.001 TYR A1067 ARG 0.008 0.001 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 36) link_NAG-ASN : angle 2.61799 ( 108) link_BETA1-4 : bond 0.00555 ( 18) link_BETA1-4 : angle 1.67360 ( 54) hydrogen bonds : bond 0.04853 ( 1237) hydrogen bonds : angle 6.32014 ( 3426) SS BOND : bond 0.00531 ( 51) SS BOND : angle 1.39813 ( 102) covalent geometry : bond 0.00467 (34951) covalent geometry : angle 0.64685 (47530) Misc. bond : bond 0.00047 ( 1) *********************** 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 298 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.9058 (t) cc_final: 0.8785 (m) REVERT: A 140 PHE cc_start: 0.8819 (p90) cc_final: 0.8392 (p90) REVERT: A 340 GLU cc_start: 0.9221 (pt0) cc_final: 0.8367 (pp20) REVERT: A 740 MET cc_start: 0.7611 (ttt) cc_final: 0.6582 (tmt) REVERT: A 983 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8641 (tmm-80) REVERT: A 1002 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 133 PHE cc_start: 0.7312 (m-80) cc_final: 0.6918 (m-80) REVERT: B 269 TYR cc_start: 0.8805 (m-80) cc_final: 0.8132 (m-80) REVERT: B 421 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.6466 (p90) REVERT: B 517 LEU cc_start: 0.8893 (tm) cc_final: 0.8668 (mm) REVERT: B 651 ILE cc_start: 0.8581 (pt) cc_final: 0.8271 (pp) REVERT: B 776 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8289 (ttpt) REVERT: B 780 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8205 (mp0) REVERT: B 1002 GLN cc_start: 0.9050 (tp40) cc_final: 0.8621 (tm-30) REVERT: C 135 PHE cc_start: 0.8531 (m-80) cc_final: 0.8288 (m-80) REVERT: C 153 MET cc_start: 0.4780 (tpp) cc_final: 0.4089 (tpp) REVERT: C 725 GLU cc_start: 0.8567 (tt0) cc_final: 0.8337 (tt0) REVERT: C 780 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8255 (mp0) REVERT: C 1050 MET cc_start: 0.9015 (ptm) cc_final: 0.8672 (ptm) REVERT: C 1092 GLU cc_start: 0.8049 (pp20) cc_final: 0.7821 (pp20) REVERT: D 81 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8368 (tpp) REVERT: E 137 ASN cc_start: 0.9103 (t0) cc_final: 0.8866 (t0) REVERT: E 172 THR cc_start: 0.9413 (p) cc_final: 0.9210 (p) REVERT: E 210 ASN cc_start: 0.8402 (p0) cc_final: 0.7833 (p0) REVERT: H 10 THR cc_start: 0.8416 (t) cc_final: 0.7491 (t) REVERT: H 79 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8087 (mp0) REVERT: H 82 ASP cc_start: 0.8880 (m-30) cc_final: 0.8455 (m-30) REVERT: H 122 ASP cc_start: 0.9348 (p0) cc_final: 0.8795 (p0) REVERT: H 210 ASN cc_start: 0.8629 (p0) cc_final: 0.8088 (p0) REVERT: K 81 GLU cc_start: 0.8996 (mp0) cc_final: 0.8724 (pm20) REVERT: K 82 ASP cc_start: 0.8415 (m-30) cc_final: 0.7903 (m-30) REVERT: K 137 ASN cc_start: 0.9161 (t0) cc_final: 0.8959 (t0) REVERT: K 187 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8793 (mm-30) REVERT: K 210 ASN cc_start: 0.8587 (p0) cc_final: 0.8106 (p0) outliers start: 23 outliers final: 9 residues processed: 292 average time/residue: 1.4413 time to fit residues: 519.6505 Evaluate side-chains 238 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 227 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain J residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 425 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 424 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 342 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.093563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.070558 restraints weight = 100724.901| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.01 r_work: 0.3096 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35057 Z= 0.153 Angle : 0.626 12.884 47794 Z= 0.310 Chirality : 0.045 0.478 5561 Planarity : 0.004 0.043 6072 Dihedral : 6.535 56.734 5760 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.45 % Favored : 93.53 % Rotamer: Outliers : 1.01 % Allowed : 10.62 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4265 helix: 2.14 (0.21), residues: 684 sheet: -0.39 (0.14), residues: 1334 loop : -1.47 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.003 0.000 HIS J 208 PHE 0.015 0.001 PHE B 106 TYR 0.020 0.001 TYR A1067 ARG 0.009 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 36) link_NAG-ASN : angle 2.45661 ( 108) link_BETA1-4 : bond 0.00525 ( 18) link_BETA1-4 : angle 1.68094 ( 54) hydrogen bonds : bond 0.04111 ( 1237) hydrogen bonds : angle 5.79750 ( 3426) SS BOND : bond 0.00432 ( 51) SS BOND : angle 1.27873 ( 102) covalent geometry : bond 0.00346 (34951) covalent geometry : angle 0.61141 (47530) Misc. bond : bond 0.00025 ( 1) *********************** 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 294 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.9062 (t) cc_final: 0.8835 (m) REVERT: A 140 PHE cc_start: 0.8864 (p90) cc_final: 0.8458 (p90) REVERT: A 740 MET cc_start: 0.7601 (ttt) cc_final: 0.6480 (tmt) REVERT: A 983 ARG cc_start: 0.8992 (ttp80) cc_final: 0.8562 (ttp80) REVERT: A 1002 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 92 PHE cc_start: 0.7930 (t80) cc_final: 0.7631 (t80) REVERT: B 153 MET cc_start: 0.6823 (ppp) cc_final: 0.5920 (ttp) REVERT: B 269 TYR cc_start: 0.8865 (m-80) cc_final: 0.8175 (m-80) REVERT: B 421 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.6411 (p90) REVERT: B 517 LEU cc_start: 0.8899 (tm) cc_final: 0.8683 (mm) REVERT: B 651 ILE cc_start: 0.8621 (pt) cc_final: 0.8305 (pp) REVERT: B 776 LYS cc_start: 0.8818 (ttpt) cc_final: 0.8332 (ttpt) REVERT: B 780 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8256 (mp0) REVERT: B 1002 GLN cc_start: 0.9039 (tp40) cc_final: 0.8645 (tm-30) REVERT: B 1092 GLU cc_start: 0.8452 (tp30) cc_final: 0.7903 (pp20) REVERT: C 135 PHE cc_start: 0.8612 (m-80) cc_final: 0.8366 (m-80) REVERT: C 153 MET cc_start: 0.4632 (tpp) cc_final: 0.3970 (tpp) REVERT: C 697 MET cc_start: 0.8631 (ptp) cc_final: 0.8352 (ptm) REVERT: C 725 GLU cc_start: 0.8621 (tt0) cc_final: 0.8387 (tt0) REVERT: C 780 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8300 (mp0) REVERT: C 1050 MET cc_start: 0.9089 (ptm) cc_final: 0.8822 (ptm) REVERT: C 1092 GLU cc_start: 0.8266 (pp20) cc_final: 0.7976 (pp20) REVERT: D 216 ASP cc_start: 0.8934 (m-30) cc_final: 0.8622 (t0) REVERT: D 220 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7417 (mm-30) REVERT: E 134 CYS cc_start: 0.8571 (t) cc_final: 0.8116 (t) REVERT: E 137 ASN cc_start: 0.9039 (t0) cc_final: 0.8763 (t0) REVERT: E 210 ASN cc_start: 0.8441 (p0) cc_final: 0.7869 (p0) REVERT: G 82 GLU cc_start: 0.8527 (tm-30) cc_final: 0.7866 (tm-30) REVERT: H 134 CYS cc_start: 0.8490 (t) cc_final: 0.8100 (t) REVERT: H 137 ASN cc_start: 0.9212 (t0) cc_final: 0.8981 (t0) REVERT: H 210 ASN cc_start: 0.8676 (p0) cc_final: 0.8104 (p0) REVERT: K 27 GLN cc_start: 0.8311 (mp10) cc_final: 0.7940 (mp10) REVERT: K 82 ASP cc_start: 0.8534 (m-30) cc_final: 0.8034 (m-30) REVERT: K 137 ASN cc_start: 0.9159 (t0) cc_final: 0.8932 (t0) REVERT: K 210 ASN cc_start: 0.8675 (p0) cc_final: 0.8214 (p0) outliers start: 38 outliers final: 18 residues processed: 285 average time/residue: 1.2275 time to fit residues: 436.3629 Evaluate side-chains 259 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 70 optimal weight: 5.9990 chunk 262 optimal weight: 0.0040 chunk 192 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 397 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 390 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 355 optimal weight: 0.0040 chunk 357 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 overall best weight: 1.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN B 239 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069333 restraints weight = 100495.376| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.09 r_work: 0.3075 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35057 Z= 0.189 Angle : 0.628 11.985 47794 Z= 0.311 Chirality : 0.045 0.480 5561 Planarity : 0.004 0.046 6072 Dihedral : 6.223 57.097 5759 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.97 % Allowed : 12.35 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4265 helix: 2.09 (0.21), residues: 693 sheet: -0.38 (0.14), residues: 1336 loop : -1.48 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.004 0.001 HIS D 208 PHE 0.015 0.001 PHE C 906 TYR 0.028 0.001 TYR E 49 ARG 0.010 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 36) link_NAG-ASN : angle 2.44358 ( 108) link_BETA1-4 : bond 0.00501 ( 18) link_BETA1-4 : angle 1.68443 ( 54) hydrogen bonds : bond 0.04012 ( 1237) hydrogen bonds : angle 5.49904 ( 3426) SS BOND : bond 0.00567 ( 51) SS BOND : angle 1.31405 ( 102) covalent geometry : bond 0.00430 (34951) covalent geometry : angle 0.61324 (47530) Misc. bond : bond 0.00041 ( 1) *********************** 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 321 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 247 time to evaluate : 4.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.9065 (t) cc_final: 0.8825 (m) REVERT: A 140 PHE cc_start: 0.8870 (p90) cc_final: 0.8483 (p90) REVERT: A 340 GLU cc_start: 0.9230 (pt0) cc_final: 0.8539 (pp20) REVERT: A 369 TYR cc_start: 0.8673 (t80) cc_final: 0.8440 (t80) REVERT: A 725 GLU cc_start: 0.8855 (tt0) cc_final: 0.8626 (tt0) REVERT: A 740 MET cc_start: 0.7638 (ttt) cc_final: 0.6638 (tmt) REVERT: B 92 PHE cc_start: 0.7931 (t80) cc_final: 0.7627 (t80) REVERT: B 269 TYR cc_start: 0.8865 (m-80) cc_final: 0.8091 (m-80) REVERT: B 421 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.6223 (p90) REVERT: B 651 ILE cc_start: 0.8606 (pt) cc_final: 0.8304 (pp) REVERT: B 776 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8312 (ttpt) REVERT: B 780 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8236 (mp0) REVERT: B 866 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7580 (p) REVERT: B 902 MET cc_start: 0.9055 (mmm) cc_final: 0.8776 (tpp) REVERT: B 1002 GLN cc_start: 0.9027 (tp40) cc_final: 0.8650 (tm-30) REVERT: C 153 MET cc_start: 0.4309 (tpp) cc_final: 0.3664 (tpp) REVERT: C 725 GLU cc_start: 0.8631 (tt0) cc_final: 0.8392 (tt0) REVERT: C 780 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8284 (mp0) REVERT: C 1092 GLU cc_start: 0.8386 (pp20) cc_final: 0.8105 (pp20) REVERT: D 216 ASP cc_start: 0.8889 (m-30) cc_final: 0.8596 (t0) REVERT: D 220 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7410 (mm-30) REVERT: E 134 CYS cc_start: 0.8504 (t) cc_final: 0.8126 (t) REVERT: E 137 ASN cc_start: 0.8992 (t0) cc_final: 0.8756 (t0) REVERT: E 210 ASN cc_start: 0.8473 (p0) cc_final: 0.7893 (p0) REVERT: G 46 GLU cc_start: 0.8416 (tt0) cc_final: 0.8037 (tt0) REVERT: G 81 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8871 (tpp) REVERT: G 82 GLU cc_start: 0.8578 (tm-30) cc_final: 0.7894 (tm-30) REVERT: H 210 ASN cc_start: 0.8684 (p0) cc_final: 0.8118 (p0) REVERT: J 74 GLU cc_start: 0.8977 (pm20) cc_final: 0.8757 (tm-30) REVERT: K 82 ASP cc_start: 0.8596 (m-30) cc_final: 0.8070 (m-30) REVERT: K 137 ASN cc_start: 0.9071 (t0) cc_final: 0.8852 (t0) REVERT: K 210 ASN cc_start: 0.8723 (p0) cc_final: 0.8260 (p0) outliers start: 74 outliers final: 30 residues processed: 309 average time/residue: 1.1689 time to fit residues: 458.3909 Evaluate side-chains 260 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 7.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 167 ASP Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 399 optimal weight: 4.9990 chunk 323 optimal weight: 4.9990 chunk 416 optimal weight: 0.9990 chunk 246 optimal weight: 0.7980 chunk 414 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 251 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.093838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.069767 restraints weight = 99174.048| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.83 r_work: 0.3117 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35057 Z= 0.123 Angle : 0.613 11.855 47794 Z= 0.300 Chirality : 0.045 0.461 5561 Planarity : 0.004 0.044 6072 Dihedral : 5.955 56.350 5759 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.73 % Allowed : 13.77 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4265 helix: 2.05 (0.21), residues: 703 sheet: -0.26 (0.14), residues: 1318 loop : -1.40 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.002 0.000 HIS A 49 PHE 0.021 0.001 PHE B 65 TYR 0.027 0.001 TYR E 49 ARG 0.009 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 36) link_NAG-ASN : angle 2.29229 ( 108) link_BETA1-4 : bond 0.00586 ( 18) link_BETA1-4 : angle 1.66281 ( 54) hydrogen bonds : bond 0.03591 ( 1237) hydrogen bonds : angle 5.29156 ( 3426) SS BOND : bond 0.00419 ( 51) SS BOND : angle 1.17849 ( 102) covalent geometry : bond 0.00278 (34951) covalent geometry : angle 0.60016 (47530) Misc. bond : bond 0.00012 ( 1) *********************** 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 324 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 259 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.9103 (t) cc_final: 0.8866 (m) REVERT: A 140 PHE cc_start: 0.8865 (p90) cc_final: 0.8479 (p90) REVERT: A 369 TYR cc_start: 0.8611 (t80) cc_final: 0.8342 (t80) REVERT: A 725 GLU cc_start: 0.8832 (tt0) cc_final: 0.8234 (tt0) REVERT: A 740 MET cc_start: 0.7646 (ttt) cc_final: 0.6634 (tmt) REVERT: A 786 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8923 (mppt) REVERT: A 1002 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 92 PHE cc_start: 0.7917 (t80) cc_final: 0.7612 (t80) REVERT: B 269 TYR cc_start: 0.8858 (m-80) cc_final: 0.8145 (m-80) REVERT: B 421 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.6279 (p90) REVERT: B 651 ILE cc_start: 0.8651 (pt) cc_final: 0.8331 (pp) REVERT: B 776 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8332 (ttpt) REVERT: B 780 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8268 (mp0) REVERT: B 866 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7665 (p) REVERT: B 1002 GLN cc_start: 0.9039 (tp40) cc_final: 0.8645 (tm-30) REVERT: C 153 MET cc_start: 0.4434 (tpp) cc_final: 0.3750 (tpp) REVERT: C 191 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: C 725 GLU cc_start: 0.8614 (tt0) cc_final: 0.8323 (tt0) REVERT: C 780 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8296 (mp0) REVERT: C 1092 GLU cc_start: 0.8414 (pp20) cc_final: 0.8119 (pp20) REVERT: D 216 ASP cc_start: 0.8741 (m-30) cc_final: 0.8508 (t0) REVERT: D 220 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7374 (mm-30) REVERT: E 33 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8918 (tp) REVERT: E 134 CYS cc_start: 0.8326 (t) cc_final: 0.7930 (t) REVERT: E 210 ASN cc_start: 0.8455 (p0) cc_final: 0.7876 (p0) REVERT: G 81 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8951 (tpp) REVERT: G 82 GLU cc_start: 0.8592 (tm-30) cc_final: 0.7916 (tm-30) REVERT: G 113 GLN cc_start: 0.9232 (pt0) cc_final: 0.8920 (pm20) REVERT: H 170 ASP cc_start: 0.8497 (p0) cc_final: 0.8296 (p0) REVERT: H 181 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8938 (pp) REVERT: H 182 SER cc_start: 0.9464 (OUTLIER) cc_final: 0.9059 (p) REVERT: H 185 ASP cc_start: 0.9535 (m-30) cc_final: 0.9204 (p0) REVERT: H 210 ASN cc_start: 0.8685 (p0) cc_final: 0.8130 (p0) REVERT: K 27 GLN cc_start: 0.8328 (mp10) cc_final: 0.7987 (mp10) REVERT: K 36 TYR cc_start: 0.9418 (m-80) cc_final: 0.9193 (m-80) REVERT: K 82 ASP cc_start: 0.8593 (m-30) cc_final: 0.8019 (m-30) REVERT: K 137 ASN cc_start: 0.9020 (t0) cc_final: 0.8818 (t0) REVERT: K 210 ASN cc_start: 0.8713 (p0) cc_final: 0.8241 (p0) outliers start: 65 outliers final: 33 residues processed: 312 average time/residue: 1.1749 time to fit residues: 464.8511 Evaluate side-chains 279 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 238 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 344 optimal weight: 3.9990 chunk 428 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 406 optimal weight: 3.9990 chunk 28 optimal weight: 0.0000 chunk 265 optimal weight: 1.9990 chunk 391 optimal weight: 0.9990 chunk 283 optimal weight: 10.0000 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 544 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN E 138 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.093407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.070362 restraints weight = 100433.839| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 4.06 r_work: 0.3086 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35057 Z= 0.172 Angle : 0.628 14.614 47794 Z= 0.308 Chirality : 0.045 0.462 5561 Planarity : 0.004 0.048 6072 Dihedral : 5.888 56.737 5759 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.89 % Allowed : 14.75 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4265 helix: 2.04 (0.21), residues: 699 sheet: -0.25 (0.14), residues: 1332 loop : -1.40 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 104 HIS 0.003 0.000 HIS D 208 PHE 0.015 0.001 PHE A 86 TYR 0.019 0.001 TYR H 49 ARG 0.012 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 36) link_NAG-ASN : angle 2.30284 ( 108) link_BETA1-4 : bond 0.00504 ( 18) link_BETA1-4 : angle 1.65291 ( 54) hydrogen bonds : bond 0.03737 ( 1237) hydrogen bonds : angle 5.23035 ( 3426) SS BOND : bond 0.00442 ( 51) SS BOND : angle 1.26399 ( 102) covalent geometry : bond 0.00393 (34951) covalent geometry : angle 0.61443 (47530) Misc. bond : bond 0.00033 ( 1) *********************** 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 313 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 242 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8889 (p90) cc_final: 0.8518 (p90) REVERT: A 369 TYR cc_start: 0.8637 (t80) cc_final: 0.8358 (t80) REVERT: A 725 GLU cc_start: 0.8883 (tt0) cc_final: 0.8299 (tt0) REVERT: A 740 MET cc_start: 0.7672 (ttt) cc_final: 0.6741 (tmt) REVERT: A 786 LYS cc_start: 0.9273 (mmmt) cc_final: 0.8919 (mppt) REVERT: A 1002 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8121 (tm-30) REVERT: B 92 PHE cc_start: 0.7929 (t80) cc_final: 0.7622 (t80) REVERT: B 133 PHE cc_start: 0.7783 (m-80) cc_final: 0.6725 (m-80) REVERT: B 153 MET cc_start: 0.6091 (pp-130) cc_final: 0.5856 (ppp) REVERT: B 269 TYR cc_start: 0.8857 (m-80) cc_final: 0.8053 (m-80) REVERT: B 421 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.6274 (p90) REVERT: B 776 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8296 (ttpt) REVERT: B 780 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8282 (mp0) REVERT: B 866 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7592 (p) REVERT: B 1002 GLN cc_start: 0.9061 (tp40) cc_final: 0.8656 (tm-30) REVERT: C 153 MET cc_start: 0.4295 (tpp) cc_final: 0.3675 (tpp) REVERT: C 191 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: C 269 TYR cc_start: 0.8992 (m-80) cc_final: 0.8723 (m-80) REVERT: C 725 GLU cc_start: 0.8662 (tt0) cc_final: 0.8419 (tt0) REVERT: C 780 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8311 (mp0) REVERT: C 1092 GLU cc_start: 0.8485 (pp20) cc_final: 0.8171 (pp20) REVERT: D 216 ASP cc_start: 0.8775 (m-30) cc_final: 0.8534 (t0) REVERT: E 33 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8924 (tp) REVERT: E 134 CYS cc_start: 0.8418 (t) cc_final: 0.8017 (t) REVERT: E 210 ASN cc_start: 0.8463 (p0) cc_final: 0.7881 (p0) REVERT: G 10 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7737 (mp0) REVERT: G 81 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8967 (tpp) REVERT: G 82 GLU cc_start: 0.8627 (tm-30) cc_final: 0.7905 (tm-30) REVERT: G 184 TYR cc_start: 0.7956 (m-10) cc_final: 0.7576 (m-10) REVERT: H 210 ASN cc_start: 0.8696 (p0) cc_final: 0.8141 (p0) REVERT: K 27 GLN cc_start: 0.8315 (mp10) cc_final: 0.7763 (mp-120) REVERT: K 82 ASP cc_start: 0.8651 (m-30) cc_final: 0.8055 (m-30) REVERT: K 172 THR cc_start: 0.9276 (p) cc_final: 0.8944 (p) REVERT: K 210 ASN cc_start: 0.8740 (p0) cc_final: 0.8264 (p0) outliers start: 71 outliers final: 42 residues processed: 301 average time/residue: 1.1583 time to fit residues: 441.4055 Evaluate side-chains 279 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 3.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 8 optimal weight: 4.9990 chunk 334 optimal weight: 0.3980 chunk 277 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 368 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN D 207 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.093382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.070562 restraints weight = 100580.557| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 4.04 r_work: 0.3090 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35057 Z= 0.164 Angle : 0.637 17.070 47794 Z= 0.311 Chirality : 0.045 0.462 5561 Planarity : 0.004 0.053 6072 Dihedral : 5.809 56.557 5759 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.13 % Allowed : 15.26 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4265 helix: 2.02 (0.21), residues: 700 sheet: -0.26 (0.14), residues: 1339 loop : -1.38 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 104 HIS 0.003 0.000 HIS D 208 PHE 0.014 0.001 PHE A 86 TYR 0.020 0.001 TYR H 49 ARG 0.012 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 36) link_NAG-ASN : angle 2.27882 ( 108) link_BETA1-4 : bond 0.00515 ( 18) link_BETA1-4 : angle 1.64927 ( 54) hydrogen bonds : bond 0.03688 ( 1237) hydrogen bonds : angle 5.17931 ( 3426) SS BOND : bond 0.00432 ( 51) SS BOND : angle 1.25349 ( 102) covalent geometry : bond 0.00375 (34951) covalent geometry : angle 0.62411 (47530) Misc. bond : bond 0.00037 ( 1) *********************** 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 319 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 239 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8885 (p90) cc_final: 0.8484 (p90) REVERT: A 369 TYR cc_start: 0.8619 (t80) cc_final: 0.8373 (t80) REVERT: A 725 GLU cc_start: 0.8853 (tt0) cc_final: 0.8263 (tt0) REVERT: A 740 MET cc_start: 0.7675 (ttt) cc_final: 0.6686 (tmt) REVERT: A 786 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8927 (mppt) REVERT: A 1002 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8556 (tm-30) REVERT: B 92 PHE cc_start: 0.7952 (t80) cc_final: 0.7655 (t80) REVERT: B 131 CYS cc_start: 0.5228 (OUTLIER) cc_final: 0.2215 (p) REVERT: B 133 PHE cc_start: 0.7935 (m-80) cc_final: 0.6786 (m-80) REVERT: B 269 TYR cc_start: 0.8859 (m-80) cc_final: 0.8037 (m-80) REVERT: B 421 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.6269 (p90) REVERT: B 776 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8301 (ttpt) REVERT: B 780 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8267 (mp0) REVERT: B 866 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7619 (p) REVERT: B 902 MET cc_start: 0.9041 (mmm) cc_final: 0.8822 (tpp) REVERT: B 1002 GLN cc_start: 0.9058 (tp40) cc_final: 0.8667 (tm-30) REVERT: C 153 MET cc_start: 0.4163 (tpp) cc_final: 0.3907 (tpp) REVERT: C 191 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: C 269 TYR cc_start: 0.8984 (m-80) cc_final: 0.8711 (m-80) REVERT: C 725 GLU cc_start: 0.8646 (tt0) cc_final: 0.8396 (tt0) REVERT: C 780 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8293 (mp0) REVERT: C 1092 GLU cc_start: 0.8506 (pp20) cc_final: 0.8198 (pp20) REVERT: D 216 ASP cc_start: 0.8667 (m-30) cc_final: 0.8447 (t0) REVERT: E 33 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8915 (tp) REVERT: E 134 CYS cc_start: 0.8392 (t) cc_final: 0.8000 (t) REVERT: E 210 ASN cc_start: 0.8454 (p0) cc_final: 0.7887 (p0) REVERT: G 81 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8988 (tpp) REVERT: G 82 GLU cc_start: 0.8635 (tm-30) cc_final: 0.7892 (tm-30) REVERT: G 113 GLN cc_start: 0.9228 (pt0) cc_final: 0.8892 (pm20) REVERT: G 184 TYR cc_start: 0.8079 (m-10) cc_final: 0.7707 (m-10) REVERT: H 185 ASP cc_start: 0.9525 (m-30) cc_final: 0.9250 (p0) REVERT: H 210 ASN cc_start: 0.8677 (p0) cc_final: 0.8115 (p0) REVERT: J 216 ASP cc_start: 0.9106 (t0) cc_final: 0.8877 (t0) REVERT: K 27 GLN cc_start: 0.8357 (mp10) cc_final: 0.8002 (mp10) REVERT: K 82 ASP cc_start: 0.8668 (m-30) cc_final: 0.8062 (m-30) REVERT: K 210 ASN cc_start: 0.8714 (p0) cc_final: 0.8231 (p0) outliers start: 80 outliers final: 45 residues processed: 304 average time/residue: 1.1839 time to fit residues: 460.9141 Evaluate side-chains 284 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 4.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 232 optimal weight: 0.4980 chunk 283 optimal weight: 9.9990 chunk 337 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.093760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.070976 restraints weight = 99982.066| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.01 r_work: 0.3099 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35057 Z= 0.146 Angle : 0.635 15.703 47794 Z= 0.310 Chirality : 0.045 0.455 5561 Planarity : 0.004 0.055 6072 Dihedral : 5.726 56.514 5759 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.79 % Allowed : 15.72 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 4265 helix: 2.01 (0.21), residues: 702 sheet: -0.23 (0.14), residues: 1338 loop : -1.35 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 104 HIS 0.003 0.000 HIS D 208 PHE 0.014 0.001 PHE A 135 TYR 0.035 0.001 TYR J 153 ARG 0.014 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 36) link_NAG-ASN : angle 2.23354 ( 108) link_BETA1-4 : bond 0.00533 ( 18) link_BETA1-4 : angle 1.64239 ( 54) hydrogen bonds : bond 0.03583 ( 1237) hydrogen bonds : angle 5.11338 ( 3426) SS BOND : bond 0.00445 ( 51) SS BOND : angle 1.34293 ( 102) covalent geometry : bond 0.00335 (34951) covalent geometry : angle 0.62205 (47530) Misc. bond : bond 0.00029 ( 1) *********************** 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 312 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 245 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8870 (p90) cc_final: 0.8506 (p90) REVERT: A 369 TYR cc_start: 0.8593 (t80) cc_final: 0.8370 (t80) REVERT: A 725 GLU cc_start: 0.8854 (tt0) cc_final: 0.8253 (tt0) REVERT: A 740 MET cc_start: 0.7668 (ttt) cc_final: 0.6749 (tmt) REVERT: A 786 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8932 (mppt) REVERT: B 92 PHE cc_start: 0.7944 (t80) cc_final: 0.7647 (t80) REVERT: B 131 CYS cc_start: 0.5330 (OUTLIER) cc_final: 0.2265 (p) REVERT: B 133 PHE cc_start: 0.7923 (m-80) cc_final: 0.6770 (m-80) REVERT: B 269 TYR cc_start: 0.8854 (m-80) cc_final: 0.8036 (m-80) REVERT: B 421 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.6280 (p90) REVERT: B 776 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8327 (ttpt) REVERT: B 780 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8259 (mp0) REVERT: B 866 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7596 (p) REVERT: B 902 MET cc_start: 0.9036 (mmm) cc_final: 0.8823 (tpp) REVERT: B 1002 GLN cc_start: 0.9049 (tp40) cc_final: 0.8675 (tm-30) REVERT: C 153 MET cc_start: 0.4198 (tpp) cc_final: 0.3948 (tpp) REVERT: C 191 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: C 269 TYR cc_start: 0.8970 (m-80) cc_final: 0.8659 (m-80) REVERT: C 489 TYR cc_start: 0.8949 (m-80) cc_final: 0.8734 (m-80) REVERT: C 697 MET cc_start: 0.8610 (ptp) cc_final: 0.8305 (ptm) REVERT: C 725 GLU cc_start: 0.8635 (tt0) cc_final: 0.8385 (tt0) REVERT: C 780 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8290 (mp0) REVERT: C 1092 GLU cc_start: 0.8512 (pp20) cc_final: 0.8202 (pp20) REVERT: D 216 ASP cc_start: 0.8643 (m-30) cc_final: 0.8438 (t0) REVERT: E 33 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8911 (tp) REVERT: E 134 CYS cc_start: 0.8502 (t) cc_final: 0.8072 (t) REVERT: E 210 ASN cc_start: 0.8420 (p0) cc_final: 0.7861 (p0) REVERT: G 10 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7743 (mp0) REVERT: G 82 GLU cc_start: 0.8636 (tm-30) cc_final: 0.7852 (tm-30) REVERT: G 113 GLN cc_start: 0.9187 (pt0) cc_final: 0.8855 (pm20) REVERT: G 184 TYR cc_start: 0.8149 (m-10) cc_final: 0.7713 (m-10) REVERT: H 93 ASN cc_start: 0.8519 (p0) cc_final: 0.8253 (t0) REVERT: H 185 ASP cc_start: 0.9523 (m-30) cc_final: 0.9237 (p0) REVERT: H 210 ASN cc_start: 0.8672 (p0) cc_final: 0.8089 (p0) REVERT: K 27 GLN cc_start: 0.8394 (mp10) cc_final: 0.8122 (mp-120) REVERT: K 33 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8733 (mt) REVERT: K 82 ASP cc_start: 0.8667 (m-30) cc_final: 0.8042 (m-30) REVERT: K 172 THR cc_start: 0.9181 (p) cc_final: 0.8903 (p) REVERT: K 210 ASN cc_start: 0.8703 (p0) cc_final: 0.8206 (p0) outliers start: 67 outliers final: 47 residues processed: 302 average time/residue: 1.1085 time to fit residues: 423.8119 Evaluate side-chains 287 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 206 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 386 optimal weight: 0.0470 chunk 162 optimal weight: 1.9990 chunk 364 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 156 optimal weight: 0.0000 chunk 320 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 349 optimal weight: 6.9990 chunk 262 optimal weight: 0.0370 overall best weight: 0.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.095081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.072897 restraints weight = 99209.989| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.86 r_work: 0.3136 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 35057 Z= 0.107 Angle : 0.631 14.536 47794 Z= 0.306 Chirality : 0.045 0.431 5561 Planarity : 0.004 0.055 6072 Dihedral : 5.549 56.293 5759 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.39 % Allowed : 16.54 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 4265 helix: 1.98 (0.21), residues: 708 sheet: -0.17 (0.14), residues: 1316 loop : -1.28 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 104 HIS 0.003 0.000 HIS B 49 PHE 0.013 0.001 PHE B 106 TYR 0.021 0.001 TYR H 49 ARG 0.014 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 36) link_NAG-ASN : angle 2.13048 ( 108) link_BETA1-4 : bond 0.00588 ( 18) link_BETA1-4 : angle 1.63112 ( 54) hydrogen bonds : bond 0.03222 ( 1237) hydrogen bonds : angle 5.00265 ( 3426) SS BOND : bond 0.00389 ( 51) SS BOND : angle 1.23752 ( 102) covalent geometry : bond 0.00240 (34951) covalent geometry : angle 0.61949 (47530) Misc. bond : bond 0.00000 ( 1) *********************** 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 318 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8853 (p90) cc_final: 0.8477 (p90) REVERT: A 725 GLU cc_start: 0.8843 (tt0) cc_final: 0.8250 (tt0) REVERT: A 740 MET cc_start: 0.7547 (ttt) cc_final: 0.6579 (tmt) REVERT: A 786 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8931 (mppt) REVERT: A 1002 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8126 (tm-30) REVERT: B 66 HIS cc_start: 0.3456 (OUTLIER) cc_final: 0.2694 (p90) REVERT: B 92 PHE cc_start: 0.7908 (t80) cc_final: 0.7642 (t80) REVERT: B 131 CYS cc_start: 0.5173 (OUTLIER) cc_final: 0.1828 (p) REVERT: B 133 PHE cc_start: 0.7854 (m-80) cc_final: 0.6750 (m-80) REVERT: B 269 TYR cc_start: 0.8830 (m-80) cc_final: 0.8105 (m-80) REVERT: B 421 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.6117 (p90) REVERT: B 776 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8299 (ttpt) REVERT: B 780 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8082 (mp0) REVERT: B 866 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7540 (p) REVERT: B 977 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8678 (tm) REVERT: B 1002 GLN cc_start: 0.9006 (tp40) cc_final: 0.8599 (tm-30) REVERT: C 153 MET cc_start: 0.4225 (tpp) cc_final: 0.3984 (tpp) REVERT: C 191 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: C 269 TYR cc_start: 0.8979 (m-80) cc_final: 0.8720 (m-80) REVERT: C 489 TYR cc_start: 0.8907 (m-80) cc_final: 0.8637 (m-80) REVERT: C 697 MET cc_start: 0.8622 (ptp) cc_final: 0.8375 (ptm) REVERT: C 725 GLU cc_start: 0.8627 (tt0) cc_final: 0.8362 (tt0) REVERT: C 780 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8287 (mp0) REVERT: C 1092 GLU cc_start: 0.8537 (pp20) cc_final: 0.8219 (pp20) REVERT: D 216 ASP cc_start: 0.8615 (m-30) cc_final: 0.8408 (t0) REVERT: E 33 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8919 (tp) REVERT: E 134 CYS cc_start: 0.8365 (t) cc_final: 0.7945 (t) REVERT: E 210 ASN cc_start: 0.8421 (p0) cc_final: 0.7864 (p0) REVERT: G 3 GLN cc_start: 0.8522 (mm110) cc_final: 0.8302 (mm-40) REVERT: G 10 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7689 (mp0) REVERT: G 73 ASP cc_start: 0.8204 (t0) cc_final: 0.7813 (OUTLIER) REVERT: G 82 GLU cc_start: 0.8685 (tm-30) cc_final: 0.7901 (tm-30) REVERT: G 113 GLN cc_start: 0.9165 (pt0) cc_final: 0.8846 (pm20) REVERT: H 10 THR cc_start: 0.8921 (m) cc_final: 0.8716 (t) REVERT: H 185 ASP cc_start: 0.9511 (m-30) cc_final: 0.9231 (p0) REVERT: H 210 ASN cc_start: 0.8665 (p0) cc_final: 0.8084 (p0) REVERT: J 216 ASP cc_start: 0.9030 (t0) cc_final: 0.8799 (t0) REVERT: K 27 GLN cc_start: 0.8446 (mp10) cc_final: 0.8126 (mm-40) REVERT: K 82 ASP cc_start: 0.8654 (m-30) cc_final: 0.8047 (m-30) REVERT: K 210 ASN cc_start: 0.8680 (p0) cc_final: 0.8166 (p0) outliers start: 52 outliers final: 39 residues processed: 313 average time/residue: 1.1850 time to fit residues: 470.9701 Evaluate side-chains 292 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 104 optimal weight: 10.0000 chunk 234 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 364 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 415 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 309 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.092502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070047 restraints weight = 99275.008| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 4.01 r_work: 0.3088 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35057 Z= 0.215 Angle : 0.661 14.544 47794 Z= 0.327 Chirality : 0.046 0.454 5561 Planarity : 0.004 0.066 6072 Dihedral : 5.658 56.648 5759 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.55 % Allowed : 16.81 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 4265 helix: 1.96 (0.21), residues: 711 sheet: -0.25 (0.14), residues: 1376 loop : -1.34 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 104 HIS 0.003 0.001 HIS D 208 PHE 0.017 0.001 PHE J 29 TYR 0.042 0.002 TYR D 32 ARG 0.015 0.001 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 36) link_NAG-ASN : angle 2.22677 ( 108) link_BETA1-4 : bond 0.00461 ( 18) link_BETA1-4 : angle 1.62464 ( 54) hydrogen bonds : bond 0.03709 ( 1237) hydrogen bonds : angle 5.08388 ( 3426) SS BOND : bond 0.00462 ( 51) SS BOND : angle 1.61711 ( 102) covalent geometry : bond 0.00495 (34951) covalent geometry : angle 0.64756 (47530) Misc. bond : bond 0.00062 ( 1) ********************** 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 295 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 237 time to evaluate : 4.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8845 (p90) cc_final: 0.8505 (p90) REVERT: A 191 GLU cc_start: 0.8342 (mp0) cc_final: 0.8126 (mp0) REVERT: A 369 TYR cc_start: 0.8583 (t80) cc_final: 0.8289 (t80) REVERT: A 725 GLU cc_start: 0.8868 (tt0) cc_final: 0.8276 (tt0) REVERT: A 740 MET cc_start: 0.7694 (ttt) cc_final: 0.6697 (tmt) REVERT: A 786 LYS cc_start: 0.9319 (mmmt) cc_final: 0.8978 (mppt) REVERT: B 92 PHE cc_start: 0.7996 (t80) cc_final: 0.7707 (t80) REVERT: B 131 CYS cc_start: 0.5419 (OUTLIER) cc_final: 0.2108 (p) REVERT: B 133 PHE cc_start: 0.7831 (m-80) cc_final: 0.6779 (m-80) REVERT: B 269 TYR cc_start: 0.8891 (m-80) cc_final: 0.7993 (m-80) REVERT: B 421 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.6309 (p90) REVERT: B 776 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8298 (ttpt) REVERT: B 780 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8253 (mp0) REVERT: B 866 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7669 (p) REVERT: B 1002 GLN cc_start: 0.9054 (tp40) cc_final: 0.8681 (tm-30) REVERT: B 1092 GLU cc_start: 0.8430 (tp30) cc_final: 0.7956 (pp20) REVERT: C 153 MET cc_start: 0.4232 (tpp) cc_final: 0.3994 (tpp) REVERT: C 191 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: C 269 TYR cc_start: 0.8947 (m-80) cc_final: 0.8588 (m-80) REVERT: C 697 MET cc_start: 0.8661 (ptp) cc_final: 0.8403 (ptm) REVERT: C 725 GLU cc_start: 0.8634 (tt0) cc_final: 0.8368 (tt0) REVERT: C 780 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8269 (mp0) REVERT: C 1092 GLU cc_start: 0.8539 (pp20) cc_final: 0.8257 (pp20) REVERT: D 216 ASP cc_start: 0.8695 (m-30) cc_final: 0.8488 (t0) REVERT: E 33 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8879 (tp) REVERT: E 134 CYS cc_start: 0.8583 (t) cc_final: 0.8167 (t) REVERT: E 210 ASN cc_start: 0.8453 (p0) cc_final: 0.7896 (p0) REVERT: G 10 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7664 (mp0) REVERT: G 82 GLU cc_start: 0.8647 (tm-30) cc_final: 0.7872 (tm-30) REVERT: G 113 GLN cc_start: 0.9185 (pt0) cc_final: 0.8885 (pm20) REVERT: H 185 ASP cc_start: 0.9506 (m-30) cc_final: 0.9224 (p0) REVERT: H 210 ASN cc_start: 0.8664 (p0) cc_final: 0.8087 (p0) REVERT: J 99 GLU cc_start: 0.8716 (pt0) cc_final: 0.8304 (pt0) REVERT: J 179 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8562 (mp10) REVERT: K 27 GLN cc_start: 0.8397 (mp10) cc_final: 0.8066 (mp-120) REVERT: K 33 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8757 (mt) REVERT: K 82 ASP cc_start: 0.8700 (m-30) cc_final: 0.8082 (m-30) REVERT: K 210 ASN cc_start: 0.8684 (p0) cc_final: 0.8170 (p0) outliers start: 58 outliers final: 44 residues processed: 290 average time/residue: 1.1979 time to fit residues: 437.3925 Evaluate side-chains 287 residues out of total 3748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 179 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 62 optimal weight: 1.9990 chunk 343 optimal weight: 0.0010 chunk 330 optimal weight: 0.9990 chunk 306 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 405 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 ASN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.094086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071638 restraints weight = 99201.392| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.90 r_work: 0.3116 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35057 Z= 0.122 Angle : 0.636 14.728 47794 Z= 0.311 Chirality : 0.045 0.443 5561 Planarity : 0.004 0.061 6072 Dihedral : 5.574 56.002 5759 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.47 % Allowed : 16.97 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 4265 helix: 1.95 (0.21), residues: 713 sheet: -0.15 (0.14), residues: 1326 loop : -1.30 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 104 HIS 0.002 0.000 HIS A 49 PHE 0.016 0.001 PHE C 135 TYR 0.022 0.001 TYR H 49 ARG 0.015 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 36) link_NAG-ASN : angle 2.13822 ( 108) link_BETA1-4 : bond 0.00549 ( 18) link_BETA1-4 : angle 1.62390 ( 54) hydrogen bonds : bond 0.03403 ( 1237) hydrogen bonds : angle 5.01609 ( 3426) SS BOND : bond 0.00414 ( 51) SS BOND : angle 1.35986 ( 102) covalent geometry : bond 0.00278 (34951) covalent geometry : angle 0.62382 (47530) Misc. bond : bond 0.00017 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30265.58 seconds wall clock time: 523 minutes 1.41 seconds (31381.41 seconds total)