Starting phenix.real_space_refine on Sun Jan 26 11:55:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zox_11329/01_2025/6zox_11329.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zox_11329/01_2025/6zox_11329.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/6zox_11329/01_2025/6zox_11329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zox_11329/01_2025/6zox_11329.map" model { file = "/net/cci-nas-00/data/ceres_data/6zox_11329/01_2025/6zox_11329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zox_11329/01_2025/6zox_11329.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= -0.000 sd= 0.006 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 117 5.16 5 C 15702 2.51 5 N 4020 2.21 5 O 4857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24696 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7938 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 47, 'TRANS': 969} Chain breaks: 7 Chain: "B" Number of atoms: 7938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7938 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 47, 'TRANS': 969} Chain breaks: 7 Chain: "C" Number of atoms: 7938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7938 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 47, 'TRANS': 969} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.61, per 1000 atoms: 0.55 Number of scatterers: 24696 At special positions: 0 Unit cell: (129.442, 138.991, 161.272, 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 117 16.00 O 4857 8.00 N 4020 7.00 C 15702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS C 987 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS B 413 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 987 " - pdb=" SG CYS C 413 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1316 " - " ASN A1074 " " NAG A1321 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1316 " - " ASN B1074 " " NAG B1321 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1316 " - " ASN C1074 " " NAG C1321 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 3.1 seconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 23.7% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 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 349 through 353 removed outlier: 3.895A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.281A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.327A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 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 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.744A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.555A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.638A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.382A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.896A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.281A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.327A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.744A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.556A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.638A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.382A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (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 349 through 353 removed outlier: 3.896A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.281A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.327A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.744A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.554A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.638A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.383A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.394A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.872A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.331A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.824A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.570A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.334A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.711A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.488A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.431A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.483A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.483A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.388A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.277A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.394A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.873A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.331A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.823A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.569A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.335A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.711A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.488A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.404A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.483A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.483A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.388A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.279A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.394A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.872A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.331A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.823A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.569A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.334A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.711A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.488A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.388A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.278A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2784 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: 10.74 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 7578 1.34 - 1.48: 7154 1.48 - 1.62: 10348 1.62 - 1.75: 12 1.75 - 1.89: 135 Bond restraints: 25227 Sorted by residual: bond pdb=" CZ ARG C 346 " pdb=" NH2 ARG C 346 " ideal model delta sigma weight residual 1.330 1.267 0.063 1.30e-02 5.92e+03 2.31e+01 bond pdb=" CZ ARG B 346 " pdb=" NH2 ARG B 346 " ideal model delta sigma weight residual 1.330 1.268 0.062 1.30e-02 5.92e+03 2.26e+01 bond pdb=" CZ ARG A 346 " pdb=" NH2 ARG A 346 " ideal model delta sigma weight residual 1.330 1.268 0.062 1.30e-02 5.92e+03 2.26e+01 bond pdb=" CB PRO B 57 " pdb=" CG PRO B 57 " ideal model delta sigma weight residual 1.492 1.297 0.195 5.00e-02 4.00e+02 1.52e+01 bond pdb=" CB PRO C 57 " pdb=" CG PRO C 57 " ideal model delta sigma weight residual 1.492 1.297 0.195 5.00e-02 4.00e+02 1.52e+01 ... (remaining 25222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 33287 4.10 - 8.21: 940 8.21 - 12.31: 51 12.31 - 16.42: 15 16.42 - 20.52: 6 Bond angle restraints: 34299 Sorted by residual: angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 134.92 -20.52 2.30e+00 1.89e-01 7.96e+01 angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 134.92 -20.52 2.30e+00 1.89e-01 7.96e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 134.87 -20.47 2.30e+00 1.89e-01 7.92e+01 angle pdb=" CA ARG A 102 " pdb=" CB ARG A 102 " pdb=" CG ARG A 102 " ideal model delta sigma weight residual 114.10 129.89 -15.79 2.00e+00 2.50e-01 6.23e+01 angle pdb=" CA ARG C 102 " pdb=" CB ARG C 102 " pdb=" CG ARG C 102 " ideal model delta sigma weight residual 114.10 129.89 -15.79 2.00e+00 2.50e-01 6.23e+01 ... (remaining 34294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 14801 17.71 - 35.42: 718 35.42 - 53.13: 236 53.13 - 70.84: 64 70.84 - 88.55: 27 Dihedral angle restraints: 15846 sinusoidal: 6975 harmonic: 8871 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual -180.00 -131.21 -48.79 0 5.00e+00 4.00e-02 9.52e+01 dihedral pdb=" CA LEU A 517 " pdb=" C LEU A 517 " pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta harmonic sigma weight residual -180.00 -131.22 -48.78 0 5.00e+00 4.00e-02 9.52e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual -180.00 -131.23 -48.77 0 5.00e+00 4.00e-02 9.51e+01 ... (remaining 15843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 3644 0.138 - 0.276: 378 0.276 - 0.414: 43 0.414 - 0.552: 12 0.552 - 0.690: 3 Chirality restraints: 4080 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 4077 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 490 " 0.070 2.00e-02 2.50e+03 6.34e-02 7.03e+01 pdb=" CG PHE A 490 " -0.142 2.00e-02 2.50e+03 pdb=" CD1 PHE A 490 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 490 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 490 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 490 " 0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A 490 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 490 " 0.070 2.00e-02 2.50e+03 6.33e-02 7.01e+01 pdb=" CG PHE B 490 " -0.142 2.00e-02 2.50e+03 pdb=" CD1 PHE B 490 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE B 490 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 490 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE B 490 " 0.029 2.00e-02 2.50e+03 pdb=" CZ PHE B 490 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 490 " 0.070 2.00e-02 2.50e+03 6.33e-02 7.01e+01 pdb=" CG PHE C 490 " -0.142 2.00e-02 2.50e+03 pdb=" CD1 PHE C 490 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE C 490 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 490 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE C 490 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE C 490 " 0.015 2.00e-02 2.50e+03 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 340 2.59 - 3.17: 20934 3.17 - 3.75: 37277 3.75 - 4.32: 53379 4.32 - 4.90: 88973 Nonbonded interactions: 200903 Sorted by model distance: nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.015 3.040 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.016 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.016 3.040 nonbonded pdb=" OG SER C 98 " pdb=" O GLU C 180 " model vdw 2.096 3.040 nonbonded pdb=" OG SER B 98 " pdb=" O GLU B 180 " model vdw 2.096 3.040 ... (remaining 200898 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = 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' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.030 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 54.070 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.130 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:10.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.011 0.195 25227 Z= 0.736 Angle : 1.607 20.522 34299 Z= 0.938 Chirality : 0.093 0.690 4080 Planarity : 0.010 0.112 4356 Dihedral : 12.343 88.548 10008 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.60 % Favored : 96.20 % Rotamer: Outliers : 0.90 % Allowed : 0.83 % Favored : 98.27 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.14), residues: 3003 helix: 0.49 (0.19), residues: 609 sheet: 0.90 (0.18), residues: 729 loop : -0.20 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.007 TRP A 64 HIS 0.013 0.004 HIS A 66 PHE 0.142 0.007 PHE A 490 TYR 0.056 0.005 TYR B 495 ARG 0.026 0.003 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 292 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7669 (t0) cc_final: 0.7344 (t0) REVERT: B 104 TRP cc_start: 0.7835 (m-90) cc_final: 0.7494 (m-90) REVERT: B 164 ASN cc_start: 0.7352 (t0) cc_final: 0.7136 (t0) REVERT: B 190 ARG cc_start: 0.7314 (ttp-170) cc_final: 0.7041 (ttp-170) REVERT: B 192 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: C 164 ASN cc_start: 0.7410 (t0) cc_final: 0.7131 (t0) REVERT: C 365 TYR cc_start: 0.8518 (m-80) cc_final: 0.8186 (m-80) outliers start: 24 outliers final: 4 residues processed: 304 average time/residue: 1.3485 time to fit residues: 476.6467 Evaluate side-chains 187 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 144 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 275 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 317 ASN A 414 GLN A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 957 GLN A 969 ASN A1071 GLN B 317 ASN B 414 GLN B 901 GLN B 926 GLN B 957 GLN B1071 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 317 ASN C 414 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 957 GLN C1071 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.151655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104945 restraints weight = 40677.125| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.04 r_work: 0.3127 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25227 Z= 0.233 Angle : 0.701 10.319 34299 Z= 0.363 Chirality : 0.052 0.402 4080 Planarity : 0.005 0.058 4356 Dihedral : 7.673 59.688 4586 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.62 % Allowed : 6.13 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.53 (0.15), residues: 3003 helix: 1.33 (0.20), residues: 648 sheet: 0.92 (0.18), residues: 717 loop : -0.27 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 886 HIS 0.007 0.001 HIS C 49 PHE 0.031 0.002 PHE A 140 TYR 0.023 0.002 TYR C 453 ARG 0.014 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8458 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 164 ASN cc_start: 0.7398 (t0) cc_final: 0.7095 (t0) REVERT: A 346 ARG cc_start: 0.7999 (tpm170) cc_final: 0.7729 (mmp-170) REVERT: A 360 ASN cc_start: 0.8756 (t0) cc_final: 0.8462 (t0) REVERT: A 492 LEU cc_start: 0.9296 (mt) cc_final: 0.9055 (mm) REVERT: A 574 ASP cc_start: 0.8216 (t0) cc_final: 0.7747 (t0) REVERT: B 52 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 88 ASP cc_start: 0.8750 (m-30) cc_final: 0.8513 (m-30) REVERT: B 164 ASN cc_start: 0.7111 (t0) cc_final: 0.6727 (t0) REVERT: B 192 PHE cc_start: 0.8429 (m-80) cc_final: 0.8114 (m-80) REVERT: B 360 ASN cc_start: 0.8762 (t0) cc_final: 0.8460 (t0) REVERT: B 574 ASP cc_start: 0.8302 (t0) cc_final: 0.7803 (t0) REVERT: C 132 GLU cc_start: 0.7766 (tt0) cc_final: 0.7470 (mm-30) REVERT: C 164 ASN cc_start: 0.7116 (t0) cc_final: 0.6763 (t0) REVERT: C 346 ARG cc_start: 0.7937 (tpm-80) cc_final: 0.7679 (tpm-80) REVERT: C 360 ASN cc_start: 0.8840 (t0) cc_final: 0.8517 (t0) REVERT: C 365 TYR cc_start: 0.8668 (m-80) cc_final: 0.8335 (m-80) REVERT: C 564 GLN cc_start: 0.7956 (tp40) cc_final: 0.7070 (tp-100) REVERT: C 731 MET cc_start: 0.9358 (ptt) cc_final: 0.9104 (ptm) REVERT: C 985 ASP cc_start: 0.8035 (t0) cc_final: 0.7826 (t0) REVERT: C 988 GLU cc_start: 0.8006 (pm20) cc_final: 0.7785 (pm20) outliers start: 43 outliers final: 15 residues processed: 260 average time/residue: 1.1956 time to fit residues: 367.0161 Evaluate side-chains 197 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 14 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 94 optimal weight: 0.0980 chunk 112 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 245 HIS A 314 GLN A 317 ASN A 901 GLN A 957 GLN A1135 ASN B 245 HIS B 317 ASN B 957 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 317 ASN C 901 GLN C 957 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.152084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101948 restraints weight = 40954.241| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.81 r_work: 0.3150 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25227 Z= 0.193 Angle : 0.609 9.326 34299 Z= 0.315 Chirality : 0.049 0.390 4080 Planarity : 0.004 0.039 4356 Dihedral : 7.034 58.975 4584 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.73 % Allowed : 8.79 % 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: 0.51 (0.15), residues: 3003 helix: 1.61 (0.21), residues: 651 sheet: 0.85 (0.18), residues: 729 loop : -0.41 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.003 0.001 HIS B1048 PHE 0.025 0.002 PHE C 140 TYR 0.014 0.001 TYR A 396 ARG 0.007 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7746 (tm-30) REVERT: A 346 ARG cc_start: 0.7965 (tpm170) cc_final: 0.7660 (mmp-170) REVERT: A 360 ASN cc_start: 0.8874 (t0) cc_final: 0.8450 (t0) REVERT: A 546 LEU cc_start: 0.7979 (tt) cc_final: 0.7543 (tt) REVERT: A 1092 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: B 52 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 88 ASP cc_start: 0.8688 (m-30) cc_final: 0.8398 (m-30) REVERT: B 132 GLU cc_start: 0.7813 (tt0) cc_final: 0.7601 (mm-30) REVERT: B 164 ASN cc_start: 0.7027 (t0) cc_final: 0.6655 (t0) REVERT: B 360 ASN cc_start: 0.8864 (t0) cc_final: 0.8455 (t0) REVERT: B 427 ASP cc_start: 0.8539 (m-30) cc_final: 0.8066 (m-30) REVERT: B 489 TYR cc_start: 0.7896 (m-80) cc_final: 0.7662 (m-10) REVERT: B 546 LEU cc_start: 0.7878 (tt) cc_final: 0.7472 (tt) REVERT: B 574 ASP cc_start: 0.8315 (t0) cc_final: 0.7824 (t0) REVERT: B 1029 MET cc_start: 0.9163 (tpp) cc_final: 0.8936 (tpp) REVERT: C 346 ARG cc_start: 0.7920 (tpm-80) cc_final: 0.7647 (tpm-80) REVERT: C 360 ASN cc_start: 0.8954 (t0) cc_final: 0.8516 (t0) REVERT: C 365 TYR cc_start: 0.8613 (m-80) cc_final: 0.8343 (m-80) REVERT: C 546 LEU cc_start: 0.7985 (tt) cc_final: 0.7540 (tt) REVERT: C 564 GLN cc_start: 0.8010 (tp40) cc_final: 0.7144 (tp-100) REVERT: C 574 ASP cc_start: 0.8306 (t0) cc_final: 0.7784 (t0) REVERT: C 731 MET cc_start: 0.9404 (ptt) cc_final: 0.9179 (ptm) REVERT: C 988 GLU cc_start: 0.7960 (pm20) cc_final: 0.7735 (pm20) outliers start: 46 outliers final: 23 residues processed: 248 average time/residue: 1.1897 time to fit residues: 354.9775 Evaluate side-chains 208 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 92 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 242 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 301 optimal weight: 0.0370 chunk 214 optimal weight: 8.9990 overall best weight: 1.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 957 GLN A1036 GLN B 317 ASN B 957 GLN B1054 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C1036 GLN C1054 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.149673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099426 restraints weight = 41068.405| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.84 r_work: 0.3082 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25227 Z= 0.254 Angle : 0.584 9.275 34299 Z= 0.303 Chirality : 0.049 0.357 4080 Planarity : 0.004 0.044 4356 Dihedral : 6.630 58.586 4582 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.29 % Allowed : 10.37 % Favored : 87.34 % 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: 0.32 (0.15), residues: 3003 helix: 1.41 (0.21), residues: 669 sheet: 0.61 (0.18), residues: 744 loop : -0.48 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS A1064 PHE 0.020 0.002 PHE C 456 TYR 0.013 0.001 TYR B1067 ARG 0.005 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5180 (OUTLIER) cc_final: 0.4723 (p) REVERT: A 52 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 314 GLN cc_start: 0.8823 (tt0) cc_final: 0.8592 (mm-40) REVERT: A 346 ARG cc_start: 0.8026 (tpm170) cc_final: 0.7744 (tpm-80) REVERT: A 360 ASN cc_start: 0.9068 (t0) cc_final: 0.8606 (t0) REVERT: A 546 LEU cc_start: 0.8023 (tt) cc_final: 0.7664 (tt) REVERT: A 556 ASN cc_start: 0.8733 (p0) cc_final: 0.8470 (m-40) REVERT: A 1092 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: B 29 THR cc_start: 0.5081 (OUTLIER) cc_final: 0.4645 (p) REVERT: B 52 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 88 ASP cc_start: 0.8663 (m-30) cc_final: 0.8400 (m-30) REVERT: B 132 GLU cc_start: 0.7774 (tt0) cc_final: 0.7478 (mm-30) REVERT: B 164 ASN cc_start: 0.7028 (t0) cc_final: 0.6709 (t0) REVERT: B 346 ARG cc_start: 0.7918 (tpm-80) cc_final: 0.7539 (tpm-80) REVERT: B 360 ASN cc_start: 0.8977 (t0) cc_final: 0.8562 (t0) REVERT: B 427 ASP cc_start: 0.8612 (m-30) cc_final: 0.8150 (m-30) REVERT: B 546 LEU cc_start: 0.7949 (tt) cc_final: 0.7711 (tt) REVERT: B 1029 MET cc_start: 0.9223 (tpp) cc_final: 0.8991 (tpp) REVERT: C 29 THR cc_start: 0.5578 (OUTLIER) cc_final: 0.5099 (p) REVERT: C 346 ARG cc_start: 0.7943 (tpm-80) cc_final: 0.7655 (tpm-80) REVERT: C 360 ASN cc_start: 0.9120 (t0) cc_final: 0.8681 (t0) REVERT: C 546 LEU cc_start: 0.7970 (tt) cc_final: 0.7713 (tt) REVERT: C 560 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8953 (tt) REVERT: C 564 GLN cc_start: 0.8119 (tp40) cc_final: 0.7196 (tp-100) REVERT: C 731 MET cc_start: 0.9466 (ptt) cc_final: 0.9171 (ptm) REVERT: C 988 GLU cc_start: 0.7968 (pm20) cc_final: 0.7694 (pm20) outliers start: 61 outliers final: 30 residues processed: 237 average time/residue: 1.1354 time to fit residues: 319.8810 Evaluate side-chains 204 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 chunk 264 optimal weight: 0.9980 chunk 253 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 275 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 317 ASN B 317 ASN B 957 GLN B1135 ASN C 99 ASN C 317 ASN C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.150832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100915 restraints weight = 41005.729| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.84 r_work: 0.3111 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25227 Z= 0.172 Angle : 0.556 9.578 34299 Z= 0.286 Chirality : 0.048 0.343 4080 Planarity : 0.004 0.052 4356 Dihedral : 6.268 58.094 4580 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.07 % Allowed : 11.46 % Favored : 86.47 % 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: 0.34 (0.15), residues: 3003 helix: 1.50 (0.21), residues: 672 sheet: 0.66 (0.19), residues: 714 loop : -0.50 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.000 HIS B1048 PHE 0.024 0.001 PHE C 456 TYR 0.014 0.001 TYR A 369 ARG 0.009 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 104 TRP cc_start: 0.8313 (m-90) cc_final: 0.8057 (m-90) REVERT: A 314 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8526 (mm-40) REVERT: A 346 ARG cc_start: 0.7976 (tpm170) cc_final: 0.7693 (tpm-80) REVERT: A 360 ASN cc_start: 0.9120 (t0) cc_final: 0.8609 (t0) REVERT: A 546 LEU cc_start: 0.7972 (tt) cc_final: 0.7642 (tt) REVERT: A 646 ARG cc_start: 0.8338 (tpt-90) cc_final: 0.8136 (tmt-80) REVERT: A 1092 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: B 52 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7853 (tm-30) REVERT: B 132 GLU cc_start: 0.7816 (tt0) cc_final: 0.7469 (mm-30) REVERT: B 164 ASN cc_start: 0.7003 (t0) cc_final: 0.6694 (t0) REVERT: B 346 ARG cc_start: 0.7897 (tpm-80) cc_final: 0.7558 (tpm-80) REVERT: B 360 ASN cc_start: 0.9025 (t0) cc_final: 0.8588 (t0) REVERT: B 427 ASP cc_start: 0.8619 (m-30) cc_final: 0.8201 (m-30) REVERT: B 546 LEU cc_start: 0.7920 (tt) cc_final: 0.7696 (tt) REVERT: B 1029 MET cc_start: 0.9150 (tpp) cc_final: 0.8923 (tpp) REVERT: C 346 ARG cc_start: 0.7878 (tpm-80) cc_final: 0.7615 (tpm-80) REVERT: C 360 ASN cc_start: 0.9144 (t0) cc_final: 0.8741 (t0) REVERT: C 546 LEU cc_start: 0.7984 (tt) cc_final: 0.7680 (tt) REVERT: C 564 GLN cc_start: 0.8083 (tp40) cc_final: 0.7184 (tp-100) REVERT: C 646 ARG cc_start: 0.8487 (tmt170) cc_final: 0.8083 (tpt-90) REVERT: C 731 MET cc_start: 0.9467 (ptt) cc_final: 0.9240 (ptm) REVERT: C 988 GLU cc_start: 0.8017 (pm20) cc_final: 0.7776 (pm20) outliers start: 55 outliers final: 26 residues processed: 230 average time/residue: 1.1449 time to fit residues: 315.3554 Evaluate side-chains 201 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 172 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 283 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 317 ASN A 450 ASN A 690 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 784 GLN B 957 GLN B1036 GLN B1101 HIS C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C1101 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.145932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097593 restraints weight = 40896.292| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.84 r_work: 0.2986 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2922 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: