Starting phenix.real_space_refine on Sun Jun 29 21:20:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws8_32750/06_2025/7ws8_32750.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws8_32750/06_2025/7ws8_32750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws8_32750/06_2025/7ws8_32750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws8_32750/06_2025/7ws8_32750.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws8_32750/06_2025/7ws8_32750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws8_32750/06_2025/7ws8_32750.cif" } resolution = 3.0 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= -0.001 sd= 0.051 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 169 5.16 5 C 22164 2.51 5 N 5701 2.21 5 O 6650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34684 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "C" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8096 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} 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: "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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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: "E" 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 Time building chain proxies: 17.98, per 1000 atoms: 0.52 Number of scatterers: 34684 At special positions: 0 Unit cell: (132.288, 158.912, 243.776, 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 169 16.00 O 6650 8.00 N 5701 7.00 C 22164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.07 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=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN B 801 " " NAG G 1 " - " ASN B1074 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1074 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN C1134 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 801 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN A1134 " Time building additional restraints: 8.18 Conformation dependent library (CDL) restraints added in 4.2 seconds 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8072 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 50 sheets defined 36.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 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: 4.260A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.143A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 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: 3.593A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.578A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.063A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.331A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.436A 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 337 through 343 removed outlier: 4.103A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.277A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.987A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.014A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 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: 3.569A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.041A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.058A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.119A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.554A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.863A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 744 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 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.594A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.020A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.865A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.597A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.673A pdb=" N LEU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 32 " --> pdb=" O PHE D 28 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 79 removed outlier: 3.729A pdb=" N LEU D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.170A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.550A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.532A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 4.418A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.603A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.669A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.646A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.523A pdb=" N MET D 383 " --> pdb=" O ILE D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.015A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.504A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.194A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.565A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.217A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 561 removed outlier: 4.067A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.541A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'E' and resid 20 through 53 Processing helix chain 'E' and resid 55 through 79 removed outlier: 3.620A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.959A pdb=" N MET E 123 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 157 through 194 removed outlier: 3.503A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.527A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 221 through 231 Processing helix chain 'E' and resid 232 through 252 removed outlier: 4.492A pdb=" N LEU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.876A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.878A pdb=" N MET E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.500A pdb=" N SER E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.685A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.758A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.060A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA E 412 " --> pdb=" O MET E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.559A pdb=" N LEU E 418 " --> pdb=" O THR E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 447 removed outlier: 3.777A pdb=" N ILE E 436 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.447A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.773A pdb=" N MET E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 503 Processing helix chain 'E' and resid 505 through 509 removed outlier: 3.713A pdb=" N ASN E 508 " --> pdb=" O HIS E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.541A pdb=" N GLN E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.688A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 removed outlier: 3.578A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.605A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.808A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.066A 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: 7.103A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.202A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.867A pdb=" N LYS A 537 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.604A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.854A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.609A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.847A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.624A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.624A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.582A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.596A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.599A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.627A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.166A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.243A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.828A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.300A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.678A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.775A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.942A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.694A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.784A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.784A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.285A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.567A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.686A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.941A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 133 through 142 removed outlier: 8.265A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.925A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.094A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.559A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.930A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.049A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.667A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.667A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.542A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.853A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.773A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.866A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.515A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.393A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1529 hydrogen bonds defined for protein. 4305 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: 15.71 Time building geometry restraints manager: 9.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8194 1.33 - 1.45: 7855 1.45 - 1.58: 19242 1.58 - 1.70: 1 1.70 - 1.82: 238 Bond restraints: 35530 Sorted by residual: bond pdb=" CA SER A 596 " pdb=" CB SER A 596 " ideal model delta sigma weight residual 1.531 1.462 0.069 1.52e-02 4.33e+03 2.04e+01 bond pdb=" N VAL A 539 " pdb=" CA VAL A 539 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.08e-02 8.57e+03 9.76e+00 bond pdb=" N ILE A 587 " pdb=" CA ILE A 587 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.47e+00 bond pdb=" N VAL A 534 " pdb=" CA VAL A 534 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.21e-02 6.83e+03 8.86e+00 bond pdb=" N LYS A 537 " pdb=" CA LYS A 537 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.18e-02 7.18e+03 8.27e+00 ... (remaining 35525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 47027 1.56 - 3.12: 1122 3.12 - 4.67: 138 4.67 - 6.23: 24 6.23 - 7.79: 6 Bond angle restraints: 48317 Sorted by residual: angle pdb=" CA PRO E 469 " pdb=" N PRO E 469 " pdb=" CD PRO E 469 " ideal model delta sigma weight residual 112.00 104.21 7.79 1.40e+00 5.10e-01 3.10e+01 angle pdb=" C CYS A 590 " pdb=" CA CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sigma weight residual 111.88 117.47 -5.59 1.41e+00 5.03e-01 1.57e+01 angle pdb=" CA SER A 591 " pdb=" C SER A 591 " pdb=" O SER A 591 " ideal model delta sigma weight residual 122.14 117.71 4.43 1.24e+00 6.50e-01 1.28e+01 angle pdb=" CA CYS B 590 " pdb=" C CYS B 590 " pdb=" O CYS B 590 " ideal model delta sigma weight residual 121.87 117.75 4.12 1.16e+00 7.43e-01 1.26e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.66 -3.96 1.22e+00 6.72e-01 1.06e+01 ... (remaining 48312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 19813 17.98 - 35.95: 1553 35.95 - 53.93: 298 53.93 - 71.90: 77 71.90 - 89.88: 35 Dihedral angle restraints: 21776 sinusoidal: 9253 harmonic: 12523 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual 93.00 33.58 59.42 1 1.00e+01 1.00e-02 4.72e+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 -32.02 -53.98 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 48.75 44.25 1 1.00e+01 1.00e-02 2.72e+01 ... (remaining 21773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 5480 0.175 - 0.350: 7 0.350 - 0.526: 2 0.526 - 0.701: 0 0.701 - 0.876: 1 Chirality restraints: 5490 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" C1 NAG D 701 " pdb=" ND2 ASN D 53 " pdb=" C2 NAG D 701 " pdb=" O5 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C1 NAG E 705 " pdb=" ND2 ASN E 432 " pdb=" C2 NAG E 705 " pdb=" O5 NAG E 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 5487 not shown) Planarity restraints: 6217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 468 " 0.092 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO E 469 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO E 469 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO E 469 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 314 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C GLN A 314 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN A 314 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 315 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 84 " 0.039 5.00e-02 4.00e+02 6.04e-02 5.85e+00 pdb=" N PRO A 85 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.033 5.00e-02 4.00e+02 ... (remaining 6214 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 725 2.69 - 3.24: 33774 3.24 - 3.79: 54632 3.79 - 4.35: 73005 4.35 - 4.90: 120684 Nonbonded interactions: 282820 Sorted by model distance: nonbonded pdb=" NH1 ARG E 482 " pdb=" OG1 THR E 608 " model vdw 2.136 3.120 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE2 GLU B 191 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OG1 THR C 114 " model vdw 2.201 3.040 ... (remaining 282815 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 14 through 518 or (resid 519 through 520 and (name N or na \ me CA or name C or name O or name CB )) or resid 521 through 1147 or resid 1301 \ through 1302)) selection = (chain 'B' and (resid 14 through 518 or (resid 519 through 520 and (name N or na \ me CA or name C or name O or name CB )) or resid 521 through 1147 or resid 1301 \ through 1302)) selection = (chain 'C' and (resid 14 through 1147 or resid 1301 through 1302)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 5.380 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: 1.300 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 75.750 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.004 0.092 35621 Z= 0.196 Angle : 0.621 20.771 48547 Z= 0.324 Chirality : 0.047 0.876 5490 Planarity : 0.004 0.134 6183 Dihedral : 13.670 89.875 13575 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.26 % Rotamer: Outliers : 0.05 % Allowed : 0.13 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.13), residues: 4228 helix: 1.02 (0.14), residues: 1409 sheet: -0.06 (0.20), residues: 674 loop : -0.55 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 461 HIS 0.003 0.001 HIS B 954 PHE 0.034 0.001 PHE B 906 TYR 0.019 0.001 TYR B 873 ARG 0.007 0.000 ARG D 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 34) link_NAG-ASN : angle 4.64190 ( 102) link_BETA1-4 : bond 0.00337 ( 14) link_BETA1-4 : angle 1.51869 ( 42) hydrogen bonds : bond 0.22296 ( 1503) hydrogen bonds : angle 8.12071 ( 4305) SS BOND : bond 0.00668 ( 43) SS BOND : angle 1.69510 ( 86) covalent geometry : bond 0.00396 (35530) covalent geometry : angle 0.57851 (48317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.3574 (p-90) cc_final: 0.3206 (p90) REVERT: B 239 GLN cc_start: 0.7572 (tt0) cc_final: 0.7075 (tt0) REVERT: C 140 PHE cc_start: 0.7612 (p90) cc_final: 0.7257 (p90) REVERT: C 1002 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7555 (tm-30) REVERT: E 62 MET cc_start: -0.0420 (tpt) cc_final: -0.0728 (tpp) REVERT: E 82 MET cc_start: 0.2977 (pmm) cc_final: -0.0849 (tmt) REVERT: E 474 MET cc_start: 0.1925 (mmm) cc_final: 0.1650 (mmm) outliers start: 2 outliers final: 1 residues processed: 211 average time/residue: 1.3483 time to fit residues: 351.8530 Evaluate side-chains 159 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 360 optimal weight: 40.0000 chunk 323 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 172 optimal weight: 0.0000 chunk 334 optimal weight: 0.7980 chunk 129 optimal weight: 0.0770 chunk 203 optimal weight: 0.4980 chunk 249 optimal weight: 7.9990 chunk 387 optimal weight: 0.9990 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 536 ASN A 804 GLN A 935 GLN A 965 GLN B 81 ASN B 188 ASN B 955 ASN B1002 GLN C 165 ASN C 474 GLN D 117 ASN D 175 GLN D 373 HIS D 524 GLN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.193085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116618 restraints weight = 69604.417| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 4.09 r_work: 0.3083 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35621 Z= 0.120 Angle : 0.573 12.698 48547 Z= 0.291 Chirality : 0.045 0.382 5490 Planarity : 0.004 0.077 6183 Dihedral : 5.648 55.344 5608 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.58 % Allowed : 5.14 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.13), residues: 4228 helix: 1.21 (0.14), residues: 1415 sheet: 0.11 (0.18), residues: 725 loop : -0.49 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 436 HIS 0.009 0.001 HIS A 207 PHE 0.019 0.001 PHE B 981 TYR 0.020 0.001 TYR B 170 ARG 0.006 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 34) link_NAG-ASN : angle 3.88079 ( 102) link_BETA1-4 : bond 0.00506 ( 14) link_BETA1-4 : angle 1.22513 ( 42) hydrogen bonds : bond 0.05207 ( 1503) hydrogen bonds : angle 5.78853 ( 4305) SS BOND : bond 0.00278 ( 43) SS BOND : angle 0.99716 ( 86) covalent geometry : bond 0.00248 (35530) covalent geometry : angle 0.54346 (48317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 3.962 Fit side-chains revert: symmetry clash REVERT: A 353 TRP cc_start: 0.4009 (p-90) cc_final: 0.3404 (p90) REVERT: A 547 LYS cc_start: 0.8441 (mttp) cc_final: 0.8207 (tptt) REVERT: A 780 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: B 133 PHE cc_start: 0.8720 (m-10) cc_final: 0.8518 (m-80) REVERT: B 239 GLN cc_start: 0.7604 (tt0) cc_final: 0.7053 (tt0) REVERT: B 950 ASP cc_start: 0.8448 (m-30) cc_final: 0.8124 (m-30) REVERT: C 140 PHE cc_start: 0.7463 (p90) cc_final: 0.7041 (p90) REVERT: C 269 TYR cc_start: 0.8172 (m-80) cc_final: 0.7760 (m-80) REVERT: C 423 TYR cc_start: 0.7563 (t80) cc_final: 0.7071 (t80) REVERT: C 934 ILE cc_start: 0.8173 (mm) cc_final: 0.7946 (mp) REVERT: C 1002 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7755 (tm-30) REVERT: D 190 MET cc_start: 0.0564 (tmt) cc_final: -0.0396 (tpp) REVERT: D 525 PHE cc_start: 0.1572 (m-10) cc_final: 0.1315 (m-10) REVERT: D 557 MET cc_start: 0.1715 (ptt) cc_final: 0.1460 (tpt) REVERT: E 62 MET cc_start: -0.0644 (tpt) cc_final: -0.0903 (tpp) REVERT: E 82 MET cc_start: 0.3566 (pmm) cc_final: 0.1034 (tmt) REVERT: E 366 MET cc_start: 0.1355 (tpp) cc_final: -0.0742 (mmt) REVERT: E 480 MET cc_start: 0.0206 (mmt) cc_final: -0.0509 (ttt) REVERT: E 524 GLN cc_start: 0.0391 (mt0) cc_final: -0.0721 (tp-100) outliers start: 22 outliers final: 8 residues processed: 209 average time/residue: 1.3825 time to fit residues: 355.3975 Evaluate side-chains 170 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain E residue 277 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 166 optimal weight: 0.9980 chunk 322 optimal weight: 20.0000 chunk 129 optimal weight: 0.0570 chunk 2 optimal weight: 3.9990 chunk 422 optimal weight: 0.0000 chunk 187 optimal weight: 3.9990 chunk 353 optimal weight: 30.0000 chunk 356 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 416 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN D 42 GLN D 175 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** 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 = 0.4573 r_free = 0.4573 target = 0.192775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.124327 restraints weight = 70899.391| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 5.61 r_work: 0.3045 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35621 Z= 0.131 Angle : 0.538 11.155 48547 Z= 0.272 Chirality : 0.044 0.378 5490 Planarity : 0.004 0.062 6183 Dihedral : 5.138 55.465 5606 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.95 % Allowed : 7.37 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.13), residues: 4228 helix: 1.25 (0.14), residues: 1423 sheet: 0.14 (0.18), residues: 728 loop : -0.44 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 436 HIS 0.009 0.001 HIS A 207 PHE 0.018 0.001 PHE B 906 TYR 0.018 0.001 TYR A1067 ARG 0.004 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 34) link_NAG-ASN : angle 3.57546 ( 102) link_BETA1-4 : bond 0.00334 ( 14) link_BETA1-4 : angle 1.14329 ( 42) hydrogen bonds : bond 0.04797 ( 1503) hydrogen bonds : angle 5.43917 ( 4305) SS BOND : bond 0.00248 ( 43) SS BOND : angle 0.96485 ( 86) covalent geometry : bond 0.00293 (35530) covalent geometry : angle 0.51135 (48317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 3.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.3991 (p-90) cc_final: 0.3572 (p90) REVERT: A 432 CYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6938 (m) REVERT: A 780 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: B 239 GLN cc_start: 0.7845 (tt0) cc_final: 0.7282 (tt0) REVERT: B 950 ASP cc_start: 0.8527 (m-30) cc_final: 0.8191 (m-30) REVERT: C 140 PHE cc_start: 0.7466 (p90) cc_final: 0.7148 (p90) REVERT: C 170 TYR cc_start: 0.7530 (t80) cc_final: 0.7289 (t80) REVERT: C 239 GLN cc_start: 0.8152 (pt0) cc_final: 0.7884 (tt0) REVERT: C 269 TYR cc_start: 0.8250 (m-80) cc_final: 0.7988 (m-80) REVERT: C 406 GLU cc_start: 0.8418 (tp30) cc_final: 0.8179 (tm-30) REVERT: C 934 ILE cc_start: 0.8317 (mm) cc_final: 0.8103 (mp) REVERT: D 55 THR cc_start: 0.3160 (OUTLIER) cc_final: 0.2674 (t) REVERT: D 110 GLU cc_start: 0.5112 (pm20) cc_final: 0.4453 (pm20) REVERT: D 255 TYR cc_start: 0.3617 (t80) cc_final: 0.2580 (m-10) REVERT: D 525 PHE cc_start: 0.1381 (m-10) cc_final: 0.1161 (m-10) REVERT: D 557 MET cc_start: 0.1741 (ptt) cc_final: 0.1521 (tpt) REVERT: E 82 MET cc_start: 0.3388 (pmm) cc_final: 0.0606 (tmt) REVERT: E 480 MET cc_start: 0.0512 (mmt) cc_final: -0.0143 (ttt) REVERT: E 524 GLN cc_start: 0.0430 (mt0) cc_final: -0.0720 (tp-100) outliers start: 36 outliers final: 20 residues processed: 215 average time/residue: 1.4246 time to fit residues: 377.3478 Evaluate side-chains 193 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 383 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 124 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 148 optimal weight: 40.0000 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 389 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.191678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124008 restraints weight = 70423.234| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 6.03 r_work: 0.2988 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 35621 Z= 0.182 Angle : 0.571 10.771 48547 Z= 0.287 Chirality : 0.045 0.377 5490 Planarity : 0.004 0.055 6183 Dihedral : 4.935 55.434 5606 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.30 % Allowed : 9.23 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.13), residues: 4228 helix: 1.24 (0.14), residues: 1434 sheet: 0.04 (0.18), residues: 728 loop : -0.52 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 436 HIS 0.009 0.001 HIS A 207 PHE 0.025 0.001 PHE B 906 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 34) link_NAG-ASN : angle 3.66460 ( 102) link_BETA1-4 : bond 0.00282 ( 14) link_BETA1-4 : angle 1.14020 ( 42) hydrogen bonds : bond 0.04888 ( 1503) hydrogen bonds : angle 5.33690 ( 4305) SS BOND : bond 0.00282 ( 43) SS BOND : angle 1.49255 ( 86) covalent geometry : bond 0.00430 (35530) covalent geometry : angle 0.54271 (48317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.4037 (p-90) cc_final: 0.3668 (p90) REVERT: A 432 CYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7233 (m) REVERT: A 780 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: B 239 GLN cc_start: 0.7895 (tt0) cc_final: 0.7331 (tt0) REVERT: B 790 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8321 (mtpt) REVERT: B 950 ASP cc_start: 0.8605 (m-30) cc_final: 0.8235 (m-30) REVERT: C 140 PHE cc_start: 0.7472 (p90) cc_final: 0.7165 (p90) REVERT: C 170 TYR cc_start: 0.7571 (t80) cc_final: 0.7246 (t80) REVERT: C 269 TYR cc_start: 0.8319 (m-80) cc_final: 0.7981 (m-80) REVERT: C 423 TYR cc_start: 0.7704 (t80) cc_final: 0.7240 (t80) REVERT: C 934 ILE cc_start: 0.8402 (mm) cc_final: 0.8160 (mp) REVERT: D 255 TYR cc_start: 0.3775 (t80) cc_final: 0.2830 (m-10) REVERT: D 525 PHE cc_start: 0.1437 (m-10) cc_final: 0.1191 (m-10) REVERT: E 82 MET cc_start: 0.3430 (pmm) cc_final: 0.0776 (tmt) REVERT: E 203 TRP cc_start: 0.0788 (OUTLIER) cc_final: 0.0588 (m-10) REVERT: E 270 MET cc_start: 0.1290 (ptm) cc_final: -0.0428 (tpt) REVERT: E 315 PHE cc_start: 0.0398 (m-10) cc_final: 0.0144 (m-10) REVERT: E 366 MET cc_start: 0.0948 (tpp) cc_final: -0.0962 (mmt) REVERT: E 474 MET cc_start: -0.1341 (mpm) cc_final: -0.1635 (mpm) REVERT: E 480 MET cc_start: 0.0733 (mmt) cc_final: 0.0195 (ttt) REVERT: E 524 GLN cc_start: 0.0399 (mt0) cc_final: -0.0695 (tp-100) outliers start: 49 outliers final: 22 residues processed: 216 average time/residue: 1.4651 time to fit residues: 388.6519 Evaluate side-chains 197 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 277 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 241 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 399 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 346 optimal weight: 40.0000 chunk 313 optimal weight: 20.0000 chunk 388 optimal weight: 20.0000 chunk 327 optimal weight: 40.0000 chunk 199 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN B1005 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.190500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.120105 restraints weight = 70046.921| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 7.22 r_work: 0.2920 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 35621 Z= 0.226 Angle : 0.594 11.178 48547 Z= 0.298 Chirality : 0.046 0.373 5490 Planarity : 0.004 0.047 6183 Dihedral : 4.942 55.592 5606 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.54 % Allowed : 10.39 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.13), residues: 4228 helix: 1.28 (0.14), residues: 1418 sheet: -0.04 (0.18), residues: 719 loop : -0.59 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 436 HIS 0.008 0.001 HIS A 207 PHE 0.027 0.002 PHE B 906 TYR 0.019 0.001 TYR C 904 ARG 0.004 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 34) link_NAG-ASN : angle 3.75360 ( 102) link_BETA1-4 : bond 0.00294 ( 14) link_BETA1-4 : angle 1.19827 ( 42) hydrogen bonds : bond 0.05081 ( 1503) hydrogen bonds : angle 5.32885 ( 4305) SS BOND : bond 0.00328 ( 43) SS BOND : angle 1.44805 ( 86) covalent geometry : bond 0.00542 (35530) covalent geometry : angle 0.56525 (48317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 180 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.4057 (p-90) cc_final: 0.3678 (p90) REVERT: A 432 CYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7363 (m) REVERT: A 780 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: A 990 GLU cc_start: 0.8114 (pp20) cc_final: 0.7543 (tm-30) REVERT: B 239 GLN cc_start: 0.7832 (tt0) cc_final: 0.7301 (tt0) REVERT: B 790 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8340 (mtpt) REVERT: C 140 PHE cc_start: 0.7391 (p90) cc_final: 0.7116 (p90) REVERT: C 170 TYR cc_start: 0.7617 (t80) cc_final: 0.7306 (t80) REVERT: C 269 TYR cc_start: 0.8311 (m-80) cc_final: 0.7997 (m-80) REVERT: C 565 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7623 (p90) REVERT: C 934 ILE cc_start: 0.8524 (mm) cc_final: 0.8231 (mp) REVERT: D 55 THR cc_start: 0.3194 (OUTLIER) cc_final: 0.2815 (t) REVERT: D 525 PHE cc_start: 0.1646 (m-10) cc_final: 0.1420 (m-80) REVERT: D 557 MET cc_start: 0.1819 (tpt) cc_final: 0.1589 (tpt) REVERT: E 62 MET cc_start: -0.1351 (OUTLIER) cc_final: -0.1580 (tpp) REVERT: E 82 MET cc_start: 0.3642 (pmm) cc_final: 0.1893 (tmt) REVERT: E 270 MET cc_start: 0.0896 (ptm) cc_final: -0.0937 (tpt) REVERT: E 315 PHE cc_start: 0.1328 (m-10) cc_final: 0.0869 (m-80) REVERT: E 474 MET cc_start: -0.1221 (mpm) cc_final: -0.1595 (mpm) REVERT: E 480 MET cc_start: 0.0335 (mmt) cc_final: -0.0089 (ttt) REVERT: E 524 GLN cc_start: 0.0179 (mt0) cc_final: -0.0805 (tp-100) outliers start: 58 outliers final: 22 residues processed: 217 average time/residue: 1.3802 time to fit residues: 377.0175 Evaluate side-chains 194 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 383 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 388 optimal weight: 20.0000 chunk 324 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 297 optimal weight: 0.6980 chunk 381 optimal weight: 30.0000 chunk 244 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 340 optimal weight: 40.0000 chunk 401 optimal weight: 6.9990 chunk 407 optimal weight: 30.0000 chunk 413 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 218 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 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 = 0.4532 r_free = 0.4532 target = 0.189602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.121212 restraints weight = 69957.109| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 6.32 r_work: 0.2939 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 35621 Z= 0.265 Angle : 0.627 11.868 48547 Z= 0.315 Chirality : 0.047 0.375 5490 Planarity : 0.004 0.060 6183 Dihedral : 5.054 55.564 5606 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.75 % Allowed : 11.43 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.13), residues: 4228 helix: 1.20 (0.14), residues: 1423 sheet: -0.09 (0.19), residues: 703 loop : -0.69 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 436 HIS 0.007 0.001 HIS A 207 PHE 0.020 0.002 PHE B 906 TYR 0.025 0.002 TYR C 904 ARG 0.004 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 34) link_NAG-ASN : angle 3.85858 ( 102) link_BETA1-4 : bond 0.00208 ( 14) link_BETA1-4 : angle 1.22872 ( 42) hydrogen bonds : bond 0.05253 ( 1503) hydrogen bonds : angle 5.35992 ( 4305) SS BOND : bond 0.00391 ( 43) SS BOND : angle 1.48247 ( 86) covalent geometry : bond 0.00637 (35530) covalent geometry : angle 0.59899 (48317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 172 time to evaluate : 3.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.4114 (p-90) cc_final: 0.3771 (p90) REVERT: A 432 CYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7099 (m) REVERT: A 780 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: A 1145 LEU cc_start: 0.8436 (mt) cc_final: 0.8020 (pp) REVERT: B 239 GLN cc_start: 0.7876 (tt0) cc_final: 0.7342 (tt0) REVERT: B 790 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8449 (mtmt) REVERT: C 140 PHE cc_start: 0.7376 (p90) cc_final: 0.7084 (p90) REVERT: C 170 TYR cc_start: 0.7673 (t80) cc_final: 0.7360 (t80) REVERT: C 269 TYR cc_start: 0.8296 (m-80) cc_final: 0.8021 (m-80) REVERT: C 423 TYR cc_start: 0.7772 (t80) cc_final: 0.7376 (t80) REVERT: C 934 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8340 (mp) REVERT: D 190 MET cc_start: 0.0880 (OUTLIER) cc_final: 0.0455 (tmt) REVERT: D 255 TYR cc_start: 0.2962 (t80) cc_final: 0.1855 (m-10) REVERT: D 557 MET cc_start: 0.1607 (tpt) cc_final: 0.1403 (tpt) REVERT: E 62 MET cc_start: -0.1844 (OUTLIER) cc_final: -0.2150 (tpp) REVERT: E 82 MET cc_start: 0.3398 (pmm) cc_final: 0.0847 (tmt) REVERT: E 315 PHE cc_start: 0.0380 (m-10) cc_final: 0.0093 (m-80) REVERT: E 360 MET cc_start: 0.2731 (OUTLIER) cc_final: 0.1469 (mtm) REVERT: E 366 MET cc_start: 0.1067 (tpp) cc_final: -0.0872 (mmt) REVERT: E 480 MET cc_start: 0.0808 (mmt) cc_final: 0.0178 (ttt) REVERT: E 524 GLN cc_start: 0.0414 (mt0) cc_final: -0.0697 (tp-100) outliers start: 66 outliers final: 33 residues processed: 215 average time/residue: 1.2485 time to fit residues: 337.8212 Evaluate side-chains 205 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 4.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 504 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 134 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 173 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 315 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 338 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 450 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 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 = 0.4546 r_free = 0.4546 target = 0.190476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122193 restraints weight = 70521.280| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 6.31 r_work: 0.2966 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35621 Z= 0.176 Angle : 0.578 15.359 48547 Z= 0.288 Chirality : 0.045 0.369 5490 Planarity : 0.004 0.045 6183 Dihedral : 4.868 55.858 5606 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.43 % Allowed : 12.41 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.13), residues: 4228 helix: 1.33 (0.14), residues: 1414 sheet: -0.04 (0.19), residues: 691 loop : -0.65 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 436 HIS 0.008 0.001 HIS A 207 PHE 0.015 0.001 PHE A 157 TYR 0.037 0.001 TYR E 454 ARG 0.004 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 34) link_NAG-ASN : angle 3.62334 ( 102) link_BETA1-4 : bond 0.00362 ( 14) link_BETA1-4 : angle 1.04847 ( 42) hydrogen bonds : bond 0.04721 ( 1503) hydrogen bonds : angle 5.21155 ( 4305) SS BOND : bond 0.00256 ( 43) SS BOND : angle 1.31786 ( 86) covalent geometry : bond 0.00416 (35530) covalent geometry : angle 0.55176 (48317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 174 time to evaluate : 3.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.4158 (p-90) cc_final: 0.3858 (p90) REVERT: A 432 CYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7168 (m) REVERT: A 780 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: A 1145 LEU cc_start: 0.8387 (mt) cc_final: 0.7996 (pp) REVERT: B 239 GLN cc_start: 0.7886 (tt0) cc_final: 0.7348 (tt0) REVERT: B 790 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8452 (mtmt) REVERT: C 140 PHE cc_start: 0.7317 (p90) cc_final: 0.7047 (p90) REVERT: C 170 TYR cc_start: 0.7695 (t80) cc_final: 0.7353 (t80) REVERT: C 200 TYR cc_start: 0.7886 (m-80) cc_final: 0.7553 (t80) REVERT: C 269 TYR cc_start: 0.8266 (m-80) cc_final: 0.7963 (m-80) REVERT: C 403 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6334 (mtm180) REVERT: C 565 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7634 (p90) REVERT: C 934 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8228 (mp) REVERT: D 190 MET cc_start: 0.1005 (OUTLIER) cc_final: 0.0612 (tmt) REVERT: D 255 TYR cc_start: 0.2829 (t80) cc_final: 0.2065 (m-10) REVERT: E 62 MET cc_start: -0.1942 (OUTLIER) cc_final: -0.2483 (ptt) REVERT: E 82 MET cc_start: 0.3388 (pmm) cc_final: 0.1091 (tmt) REVERT: E 315 PHE cc_start: 0.0403 (m-10) cc_final: 0.0128 (m-80) REVERT: E 366 MET cc_start: 0.0931 (tpp) cc_final: -0.0980 (mmt) REVERT: E 474 MET cc_start: -0.1415 (mpm) cc_final: -0.1634 (mpm) REVERT: E 480 MET cc_start: 0.0824 (mmt) cc_final: 0.0204 (ttt) REVERT: E 524 GLN cc_start: 0.0410 (mt0) cc_final: -0.0704 (tp-100) outliers start: 54 outliers final: 28 residues processed: 212 average time/residue: 1.2292 time to fit residues: 328.5073 Evaluate side-chains 204 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 519 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 230 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 chunk 395 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 339 optimal weight: 40.0000 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 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 = 0.4552 r_free = 0.4552 target = 0.191037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.122992 restraints weight = 70253.710| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 5.81 r_work: 0.3002 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35621 Z= 0.141 Angle : 0.565 14.625 48547 Z= 0.282 Chirality : 0.044 0.366 5490 Planarity : 0.004 0.044 6183 Dihedral : 4.715 55.734 5606 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.19 % Allowed : 12.88 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.13), residues: 4228 helix: 1.39 (0.14), residues: 1427 sheet: 0.00 (0.19), residues: 697 loop : -0.57 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 436 HIS 0.008 0.001 HIS A 207 PHE 0.024 0.001 PHE B 981 TYR 0.031 0.001 TYR E 454 ARG 0.008 0.000 ARG D 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 34) link_NAG-ASN : angle 3.48330 ( 102) link_BETA1-4 : bond 0.00342 ( 14) link_BETA1-4 : angle 1.00495 ( 42) hydrogen bonds : bond 0.04434 ( 1503) hydrogen bonds : angle 5.10315 ( 4305) SS BOND : bond 0.00439 ( 43) SS BOND : angle 2.00260 ( 86) covalent geometry : bond 0.00326 (35530) covalent geometry : angle 0.53569 (48317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7199 (m) REVERT: A 350 VAL cc_start: 0.4317 (OUTLIER) cc_final: 0.3532 (p) REVERT: A 353 TRP cc_start: 0.4185 (p-90) cc_final: 0.3931 (p90) REVERT: A 432 CYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6886 (m) REVERT: A 661 GLU cc_start: 0.8425 (mp0) cc_final: 0.8173 (mm-30) REVERT: A 780 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: A 990 GLU cc_start: 0.8091 (pp20) cc_final: 0.7460 (tm-30) REVERT: A 1145 LEU cc_start: 0.8405 (mt) cc_final: 0.8008 (pp) REVERT: B 239 GLN cc_start: 0.7970 (tt0) cc_final: 0.7423 (tt0) REVERT: B 790 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8456 (mtmt) REVERT: B 950 ASP cc_start: 0.8607 (m-30) cc_final: 0.8268 (m-30) REVERT: C 140 PHE cc_start: 0.7305 (p90) cc_final: 0.7068 (p90) REVERT: C 170 TYR cc_start: 0.7636 (t80) cc_final: 0.7280 (t80) REVERT: C 197 ILE cc_start: 0.8985 (mm) cc_final: 0.8473 (mp) REVERT: C 200 TYR cc_start: 0.7852 (m-80) cc_final: 0.7541 (t80) REVERT: C 269 TYR cc_start: 0.8274 (m-80) cc_final: 0.8015 (m-80) REVERT: C 934 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8193 (mp) REVERT: D 190 MET cc_start: 0.1132 (OUTLIER) cc_final: 0.0669 (tmt) REVERT: D 255 TYR cc_start: 0.2759 (t80) cc_final: 0.1950 (m-10) REVERT: E 82 MET cc_start: 0.3445 (pmm) cc_final: 0.0864 (tmt) REVERT: E 190 MET cc_start: -0.0138 (OUTLIER) cc_final: -0.0420 (ptm) REVERT: E 366 MET cc_start: 0.1182 (tpp) cc_final: -0.0946 (mmm) REVERT: E 474 MET cc_start: -0.1395 (mpm) cc_final: -0.1606 (mpm) REVERT: E 524 GLN cc_start: 0.0447 (mt0) cc_final: -0.0672 (tp-100) outliers start: 45 outliers final: 25 residues processed: 210 average time/residue: 1.2877 time to fit residues: 336.4800 Evaluate side-chains 205 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 519 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 416 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 chunk 309 optimal weight: 7.9990 chunk 265 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 206 optimal weight: 30.0000 chunk 274 optimal weight: 2.9990 chunk 418 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 125 ASN B 245 HIS B1002 GLN C 239 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN D 442 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.187799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109689 restraints weight = 70317.037| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 4.45 r_work: 0.2906 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.075 35621 Z= 0.413 Angle : 0.746 15.227 48547 Z= 0.374 Chirality : 0.052 0.385 5490 Planarity : 0.005 0.052 6183 Dihedral : 5.361 55.854 5606 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.35 % Allowed : 13.07 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.12), residues: 4228 helix: 1.06 (0.14), residues: 1419 sheet: -0.32 (0.18), residues: 706 loop : -0.84 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 436 HIS 0.008 0.002 HIS B1058 PHE 0.030 0.002 PHE C1121 TYR 0.032 0.002 TYR E 454 ARG 0.005 0.001 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00844 ( 34) link_NAG-ASN : angle 4.16568 ( 102) link_BETA1-4 : bond 0.00294 ( 14) link_BETA1-4 : angle 1.51174 ( 42) hydrogen bonds : bond 0.06046 ( 1503) hydrogen bonds : angle 5.50379 ( 4305) SS BOND : bond 0.00429 ( 43) SS BOND : angle 2.10996 ( 86) covalent geometry : bond 0.00996 (35530) covalent geometry : angle 0.71562 (48317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.4213 (p-90) cc_final: 0.3966 (p90) REVERT: A 432 CYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7229 (m) REVERT: A 1145 LEU cc_start: 0.8408 (mt) cc_final: 0.8050 (pp) REVERT: B 239 GLN cc_start: 0.7833 (tt0) cc_final: 0.7333 (tt0) REVERT: C 140 PHE cc_start: 0.7367 (p90) cc_final: 0.7027 (p90) REVERT: C 170 TYR cc_start: 0.7676 (t80) cc_final: 0.7293 (t80) REVERT: C 200 TYR cc_start: 0.7979 (m-80) cc_final: 0.7685 (t80) REVERT: C 269 TYR cc_start: 0.8201 (m-80) cc_final: 0.7852 (m-80) REVERT: C 403 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6259 (mtm180) REVERT: D 190 MET cc_start: 0.0905 (OUTLIER) cc_final: 0.0624 (tmt) REVERT: D 255 TYR cc_start: 0.3478 (t80) cc_final: 0.2874 (m-10) REVERT: E 82 MET cc_start: 0.3745 (pmm) cc_final: 0.2089 (tmt) REVERT: E 315 PHE cc_start: 0.1441 (m-10) cc_final: 0.0827 (m-80) REVERT: E 366 MET cc_start: 0.0803 (tpp) cc_final: -0.0763 (mmt) REVERT: E 474 MET cc_start: -0.1027 (OUTLIER) cc_final: -0.1467 (mpm) REVERT: E 480 MET cc_start: 0.0188 (mmt) cc_final: -0.0232 (ttt) REVERT: E 524 GLN cc_start: 0.0188 (mt0) cc_final: -0.0807 (tp-100) outliers start: 51 outliers final: 31 residues processed: 205 average time/residue: 1.2016 time to fit residues: 310.1002 Evaluate side-chains 197 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 519 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7342 > 50: distance: 8 - 205: 29.630 distance: 11 - 202: 29.616 distance: 21 - 187: 35.143 distance: 118 - 142: 25.532 distance: 121 - 139: 18.645 distance: 135 - 139: 16.907 distance: 139 - 140: 10.475 distance: 140 - 141: 9.596 distance: 140 - 143: 15.455 distance: 141 - 142: 13.119 distance: 141 - 146: 31.791 distance: 143 - 144: 35.144 distance: 143 - 145: 41.926 distance: 147 - 148: 37.079 distance: 147 - 150: 46.730 distance: 148 - 153: 8.050 distance: 150 - 151: 27.970 distance: 150 - 152: 41.185 distance: 153 - 154: 12.214 distance: 154 - 155: 21.689 distance: 154 - 157: 24.712 distance: 155 - 156: 13.478 distance: 155 - 165: 12.783 distance: 157 - 158: 15.452 distance: 158 - 159: 8.533 distance: 158 - 160: 49.191 distance: 159 - 161: 13.592 distance: 160 - 162: 10.428 distance: 161 - 163: 38.552 distance: 162 - 163: 14.881 distance: 163 - 164: 41.891 distance: 165 - 166: 4.825 distance: 166 - 167: 20.388 distance: 166 - 169: 4.858 distance: 167 - 168: 22.521 distance: 167 - 172: 39.502 distance: 169 - 170: 39.335 distance: 169 - 171: 35.837 distance: 172 - 173: 15.819 distance: 172 - 178: 46.539 distance: 173 - 174: 14.293 distance: 173 - 176: 33.667 distance: 174 - 175: 28.296 distance: 174 - 179: 7.389 distance: 176 - 177: 21.576 distance: 177 - 178: 11.288 distance: 179 - 180: 15.142 distance: 180 - 181: 26.999 distance: 180 - 183: 4.551 distance: 181 - 182: 29.522 distance: 181 - 184: 15.347 distance: 184 - 185: 8.136 distance: 185 - 186: 20.273 distance: 185 - 188: 8.568 distance: 186 - 187: 18.494 distance: 186 - 193: 18.679 distance: 188 - 189: 17.009 distance: 189 - 190: 28.218 distance: 190 - 191: 13.246 distance: 190 - 192: 23.325 distance: 193 - 194: 16.324 distance: 194 - 195: 7.921 distance: 194 - 197: 25.449 distance: 195 - 196: 38.300 distance: 195 - 202: 16.885 distance: 197 - 198: 8.098 distance: 198 - 199: 18.899 distance: 199 - 200: 16.649 distance: 199 - 201: 6.369 distance: 202 - 203: 10.364 distance: 203 - 204: 31.456 distance: 203 - 206: 6.190 distance: 204 - 205: 17.736 distance: 204 - 211: 22.792 distance: 207 - 208: 11.715 distance: 208 - 209: 10.643 distance: 209 - 210: 4.856 distance: 211 - 212: 11.439 distance: 212 - 213: 7.652 distance: 212 - 215: 14.208 distance: 213 - 214: 12.213 distance: 213 - 219: 18.044 distance: 215 - 216: 8.547 distance: 216 - 217: 7.670 distance: 216 - 218: 10.352 distance: 218 - 253: 23.662