Starting phenix.real_space_refine on Mon Sep 30 10:20:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp0_11332/09_2024/6zp0_11332.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp0_11332/09_2024/6zp0_11332.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp0_11332/09_2024/6zp0_11332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp0_11332/09_2024/6zp0_11332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp0_11332/09_2024/6zp0_11332.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp0_11332/09_2024/6zp0_11332.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 111 5.16 5 C 15867 2.51 5 N 4071 2.21 5 O 4908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 191 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24957 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8039 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 48, 'TRANS': 981} Chain breaks: 6 Chain: "B" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8039 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 48, 'TRANS': 981} Chain breaks: 6 Chain: "C" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8039 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 48, 'TRANS': 981} Chain breaks: 6 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 13.46, per 1000 atoms: 0.54 Number of scatterers: 24957 At special positions: 0 Unit cell: (129.442, 142.174, 174.004, 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 111 16.00 O 4908 8.00 N 4071 7.00 C 15867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 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=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.06 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.06 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=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.06 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.06 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=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.06 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1315 " - " ASN A1074 " " NAG A1320 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1315 " - " ASN B1074 " " NAG B1320 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1315 " - " ASN C1074 " " NAG C1320 " - " ASN C 165 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 6.97 Conformation dependent library (CDL) restraints added in 3.3 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5784 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 25.1% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 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: 3.806A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.469A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.312A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 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 removed outlier: 3.688A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) 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: 3.601A 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: 3.503A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (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 removed outlier: 3.952A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.075A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.555A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (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: 3.805A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.469A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.312A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 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 removed outlier: 3.688A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.602A 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: 3.502A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (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 removed outlier: 3.953A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.075A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.555A 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 349 through 353 removed outlier: 3.806A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.470A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.312A 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 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.689A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) 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: 3.601A 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: 3.502A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (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 removed outlier: 3.953A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.075A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.555A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.118A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.769A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.302A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.124A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 140 removed outlier: 8.275A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.712A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.336A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.676A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.201A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.569A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.524A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.524A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.550A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.674A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.118A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.769A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.302A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.123A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 134 through 140 removed outlier: 8.276A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.712A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.677A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.201A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.643A 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: 3.523A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.452A 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: 4.550A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.674A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.117A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.301A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.124A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 134 through 140 removed outlier: 8.277A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.712A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.677A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (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: 6.201A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.642A 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: 3.524A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.644A 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: 3.524A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.452A 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: 4.550A 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: 4.674A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 987 hydrogen bonds defined for protein. 2727 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: 11.90 Time building geometry restraints manager: 8.02 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: 7618 1.34 - 1.48: 7107 1.48 - 1.62: 10628 1.62 - 1.75: 12 1.75 - 1.89: 129 Bond restraints: 25494 Sorted by residual: bond pdb=" CB LYS A 378 " pdb=" CG LYS A 378 " ideal model delta sigma weight residual 1.520 1.417 0.103 3.00e-02 1.11e+03 1.18e+01 bond pdb=" CB LYS C 378 " pdb=" CG LYS C 378 " ideal model delta sigma weight residual 1.520 1.417 0.103 3.00e-02 1.11e+03 1.18e+01 bond pdb=" CB LYS B 378 " pdb=" CG LYS B 378 " ideal model delta sigma weight residual 1.520 1.418 0.102 3.00e-02 1.11e+03 1.17e+01 bond pdb=" CE LYS B 378 " pdb=" NZ LYS B 378 " ideal model delta sigma weight residual 1.489 1.387 0.102 3.00e-02 1.11e+03 1.16e+01 bond pdb=" CE LYS C 378 " pdb=" NZ LYS C 378 " ideal model delta sigma weight residual 1.489 1.387 0.102 3.00e-02 1.11e+03 1.15e+01 ... (remaining 25489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.84: 34542 6.84 - 13.67: 105 13.67 - 20.51: 21 20.51 - 27.34: 0 27.34 - 34.18: 3 Bond angle restraints: 34671 Sorted by residual: angle pdb=" CB MET A 177 " pdb=" CG MET A 177 " pdb=" SD MET A 177 " ideal model delta sigma weight residual 112.70 146.88 -34.18 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB MET C 177 " pdb=" CG MET C 177 " pdb=" SD MET C 177 " ideal model delta sigma weight residual 112.70 146.87 -34.17 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB MET B 177 " pdb=" CG MET B 177 " pdb=" SD MET B 177 " ideal model delta sigma weight residual 112.70 146.87 -34.17 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CD ARG B 466 " pdb=" NE ARG B 466 " pdb=" CZ ARG B 466 " ideal model delta sigma weight residual 124.40 138.16 -13.76 1.40e+00 5.10e-01 9.66e+01 angle pdb=" CD ARG C 466 " pdb=" NE ARG C 466 " pdb=" CZ ARG C 466 " ideal model delta sigma weight residual 124.40 138.16 -13.76 1.40e+00 5.10e-01 9.65e+01 ... (remaining 34666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 14895 17.48 - 34.96: 726 34.96 - 52.43: 237 52.43 - 69.91: 84 69.91 - 87.39: 27 Dihedral angle restraints: 15969 sinusoidal: 6984 harmonic: 8985 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 171.95 -78.95 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 171.95 -78.95 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 171.92 -78.92 1 1.00e+01 1.00e-02 7.76e+01 ... (remaining 15966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3633 0.109 - 0.218: 429 0.218 - 0.326: 30 0.326 - 0.435: 15 0.435 - 0.544: 9 Chirality restraints: 4116 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.25e+00 ... (remaining 4113 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " 0.488 9.50e-02 1.11e+02 2.32e-01 1.04e+02 pdb=" NE ARG A 466 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " 0.144 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 466 " 0.487 9.50e-02 1.11e+02 2.32e-01 1.04e+02 pdb=" NE ARG C 466 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ARG C 466 " 0.144 2.00e-02 2.50e+03 pdb=" NH1 ARG C 466 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG C 466 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 466 " 0.487 9.50e-02 1.11e+02 2.32e-01 1.04e+02 pdb=" NE ARG B 466 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ARG B 466 " 0.144 2.00e-02 2.50e+03 pdb=" NH1 ARG B 466 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG B 466 " -0.036 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1043 2.70 - 3.25: 24106 3.25 - 3.80: 39536 3.80 - 4.35: 51286 4.35 - 4.90: 86529 Nonbonded interactions: 202500 Sorted by model distance: nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.154 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.155 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.155 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.187 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.188 3.040 ... (remaining 202495 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' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 59.700 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.120 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.009 0.116 25494 Z= 0.569 Angle : 1.390 34.178 34671 Z= 0.746 Chirality : 0.076 0.544 4116 Planarity : 0.009 0.232 4416 Dihedral : 12.627 87.391 10068 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.56 % Allowed : 0.56 % Favored : 98.89 % Cbeta Deviations : 0.31 % 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: 0.03 (0.14), residues: 3048 helix: 0.15 (0.18), residues: 669 sheet: 0.79 (0.17), residues: 726 loop : -0.31 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 886 HIS 0.008 0.002 HIS C1083 PHE 0.054 0.004 PHE A 65 TYR 0.033 0.004 TYR A 612 ARG 0.150 0.004 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 230 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0802 (OUTLIER) cc_final: -0.1640 (mtm) REVERT: A 979 ASP cc_start: 0.7591 (t0) cc_final: 0.7314 (t0) REVERT: B 177 MET cc_start: -0.0866 (OUTLIER) cc_final: -0.1757 (mtm) REVERT: B 979 ASP cc_start: 0.7773 (t0) cc_final: 0.7330 (t0) REVERT: C 177 MET cc_start: -0.0962 (OUTLIER) cc_final: -0.1635 (mtm) REVERT: C 979 ASP cc_start: 0.7696 (t0) cc_final: 0.7334 (t0) outliers start: 15 outliers final: 0 residues processed: 235 average time/residue: 1.2966 time to fit residues: 354.6696 Evaluate side-chains 146 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain C residue 177 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 157 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 0.0980 chunk 180 optimal weight: 0.6980 chunk 280 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 613 GLN B1010 GLN C 613 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25494 Z= 0.267 Angle : 0.664 9.692 34671 Z= 0.339 Chirality : 0.050 0.343 4116 Planarity : 0.004 0.053 4416 Dihedral : 7.276 58.101 4569 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.89 % Allowed : 5.90 % Favored : 93.21 % 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: 0.50 (0.14), residues: 3048 helix: 1.30 (0.21), residues: 684 sheet: 1.03 (0.18), residues: 699 loop : -0.36 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 104 HIS 0.005 0.001 HIS B 207 PHE 0.013 0.001 PHE A 377 TYR 0.020 0.002 TYR B 873 ARG 0.007 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 2.825 Fit side-chains REVERT: A 979 ASP cc_start: 0.7680 (t0) cc_final: 0.7412 (t0) REVERT: B 104 TRP cc_start: 0.7544 (m-90) cc_final: 0.7318 (m-90) REVERT: B 979 ASP cc_start: 0.7821 (t0) cc_final: 0.7317 (t0) REVERT: B 985 ASP cc_start: 0.7499 (p0) cc_final: 0.7283 (p0) REVERT: C 979 ASP cc_start: 0.7745 (t0) cc_final: 0.7358 (t0) REVERT: C 985 ASP cc_start: 0.7215 (p0) cc_final: 0.6963 (p0) outliers start: 24 outliers final: 6 residues processed: 187 average time/residue: 1.1632 time to fit residues: 258.4363 Evaluate side-chains 157 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 233 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 77 optimal weight: 0.0870 chunk 281 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 250 optimal weight: 20.0000 chunk 278 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 501 ASN B 901 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 901 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25494 Z= 0.258 Angle : 0.584 9.519 34671 Z= 0.294 Chirality : 0.048 0.369 4116 Planarity : 0.004 0.055 4416 Dihedral : 6.650 59.270 4560 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.52 % Allowed : 6.94 % Favored : 91.54 % 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: 0.45 (0.15), residues: 3048 helix: 1.46 (0.21), residues: 705 sheet: 0.81 (0.18), residues: 702 loop : -0.42 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 104 HIS 0.003 0.001 HIS B 207 PHE 0.012 0.001 PHE C 377 TYR 0.025 0.002 TYR B 873 ARG 0.009 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 2.889 Fit side-chains revert: symmetry clash REVERT: A 383 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.7869 (m) REVERT: A 979 ASP cc_start: 0.7718 (t0) cc_final: 0.7445 (t0) REVERT: B 104 TRP cc_start: 0.7579 (m-90) cc_final: 0.7081 (m-90) REVERT: B 979 ASP cc_start: 0.7839 (t0) cc_final: 0.7349 (OUTLIER) REVERT: C 979 ASP cc_start: 0.7778 (t0) cc_final: 0.7414 (t0) outliers start: 41 outliers final: 11 residues processed: 198 average time/residue: 1.0488 time to fit residues: 251.1206 Evaluate side-chains 167 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.7980 chunk 211 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 282 optimal weight: 0.6980 chunk 298 optimal weight: 0.7980 chunk 147 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25494 Z= 0.324 Angle : 0.594 9.593 34671 Z= 0.295 Chirality : 0.048 0.360 4116 Planarity : 0.003 0.033 4416 Dihedral : 6.317 58.611 4560 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.97 % Allowed : 7.87 % Favored : 90.16 % 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: 0.31 (0.15), residues: 3048 helix: 1.50 (0.21), residues: 702 sheet: 0.72 (0.18), residues: 660 loop : -0.55 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 104 HIS 0.004 0.001 HIS A1058 PHE 0.020 0.001 PHE C 456 TYR 0.030 0.002 TYR C 873 ARG 0.008 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 167 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8102 (m) REVERT: A 979 ASP cc_start: 0.7886 (t0) cc_final: 0.7599 (t0) REVERT: B 309 GLU cc_start: 0.8036 (mp0) cc_final: 0.7761 (mp0) REVERT: B 979 ASP cc_start: 0.7843 (t0) cc_final: 0.7405 (t0) REVERT: C 979 ASP cc_start: 0.7791 (t0) cc_final: 0.7437 (t0) outliers start: 53 outliers final: 32 residues processed: 204 average time/residue: 1.1158 time to fit residues: 273.1731 Evaluate side-chains 182 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 20.0000 chunk 169 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 268 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN C 196 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25494 Z= 0.245 Angle : 0.554 9.853 34671 Z= 0.276 Chirality : 0.047 0.357 4116 Planarity : 0.003 0.047 4416 Dihedral : 5.860 55.698 4560 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.89 % Allowed : 9.47 % Favored : 88.64 % 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 (0.15), residues: 3048 helix: 1.58 (0.21), residues: 702 sheet: 0.55 (0.18), residues: 693 loop : -0.53 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 104 HIS 0.003 0.001 HIS B1064 PHE 0.020 0.001 PHE C 456 TYR 0.014 0.001 TYR A1067 ARG 0.008 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.8135 (m) REVERT: A 979 ASP cc_start: 0.7841 (t0) cc_final: 0.7572 (t0) REVERT: B 104 TRP cc_start: 0.7704 (m-90) cc_final: 0.7236 (m-90) REVERT: B 309 GLU cc_start: 0.8003 (mp0) cc_final: 0.7759 (mp0) REVERT: B 979 ASP cc_start: 0.7852 (t0) cc_final: 0.7415 (t0) REVERT: C 979 ASP cc_start: 0.7847 (t0) cc_final: 0.7505 (t0) outliers start: 51 outliers final: 33 residues processed: 209 average time/residue: 1.0976 time to fit residues: 274.1804 Evaluate side-chains 190 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 5.9990 chunk 268 optimal weight: 0.0770 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 24 optimal weight: 0.0870 chunk 98 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25494 Z= 0.238 Angle : 0.557 10.048 34671 Z= 0.277 Chirality : 0.047 0.353 4116 Planarity : 0.003 0.033 4416 Dihedral : 5.562 55.760 4560 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.63 % Allowed : 10.13 % Favored : 88.23 % 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: 3048 helix: 1.63 (0.21), residues: 702 sheet: 0.52 (0.18), residues: 687 loop : -0.53 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.003 0.001 HIS B1064 PHE 0.012 0.001 PHE B 456 TYR 0.027 0.001 TYR A 380 ARG 0.004 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.7920 (t0) cc_final: 0.7647 (t0) REVERT: B 309 GLU cc_start: 0.7992 (mp0) cc_final: 0.7759 (mp0) REVERT: B 979 ASP cc_start: 0.7863 (t0) cc_final: 0.7430 (t0) REVERT: C 979 ASP cc_start: 0.7852 (t0) cc_final: 0.7507 (t0) outliers start: 44 outliers final: 33 residues processed: 204 average time/residue: 1.1304 time to fit residues: 274.6214 Evaluate side-chains 190 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 218 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 297 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 957 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25494 Z= 0.170 Angle : 0.531 10.589 34671 Z= 0.265 Chirality : 0.046 0.350 4116 Planarity : 0.003 0.033 4416 Dihedral : 5.185 55.780 4560 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.71 % Allowed : 10.80 % Favored : 87.49 % 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: 0.48 (0.15), residues: 3048 helix: 1.84 (0.21), residues: 696 sheet: 0.61 (0.19), residues: 660 loop : -0.43 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 104 HIS 0.002 0.001 HIS B1064 PHE 0.018 0.001 PHE A 168 TYR 0.033 0.001 TYR C 380 ARG 0.014 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 167 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8700 (ttp80) cc_final: 0.8450 (tmm-80) REVERT: A 979 ASP cc_start: 0.7925 (t0) cc_final: 0.7649 (t0) REVERT: B 309 GLU cc_start: 0.7961 (mp0) cc_final: 0.7739 (mp0) REVERT: B 408 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8389 (tmm-80) REVERT: B 979 ASP cc_start: 0.7867 (t0) cc_final: 0.7434 (t0) REVERT: C 177 MET cc_start: 0.2820 (tpp) cc_final: 0.2422 (tmt) REVERT: C 408 ARG cc_start: 0.8745 (ttp80) cc_final: 0.8514 (tmm-80) REVERT: C 979 ASP cc_start: 0.7857 (t0) cc_final: 0.7515 (t0) outliers start: 46 outliers final: 32 residues processed: 203 average time/residue: 1.0917 time to fit residues: 266.7377 Evaluate side-chains 188 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25494 Z= 0.274 Angle : 0.559 10.545 34671 Z= 0.279 Chirality : 0.047 0.347 4116 Planarity : 0.003 0.033 4416 Dihedral : 5.076 55.782 4560 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.74 % 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: 0.35 (0.15), residues: 3048 helix: 1.68 (0.21), residues: 699 sheet: 0.47 (0.18), residues: 663 loop : -0.47 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 104 HIS 0.003 0.001 HIS B1064 PHE 0.014 0.001 PHE A 759 TYR 0.025 0.001 TYR C 380 ARG 0.007 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8455 (tmm-80) REVERT: A 979 ASP cc_start: 0.7946 (t0) cc_final: 0.7669 (t0) REVERT: B 309 GLU cc_start: 0.8000 (mp0) cc_final: 0.7770 (mp0) REVERT: B 979 ASP cc_start: 0.7881 (t0) cc_final: 0.7465 (t0) REVERT: C 979 ASP cc_start: 0.7898 (t0) cc_final: 0.7540 (t0) outliers start: 47 outliers final: 36 residues processed: 199 average time/residue: 1.1239 time to fit residues: 273.0567 Evaluate side-chains 186 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 4.9990 chunk 285 optimal weight: 0.8980 chunk 260 optimal weight: 3.9990 chunk 277 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 250 optimal weight: 0.0980 chunk 262 optimal weight: 8.9990 chunk 276 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25494 Z= 0.210 Angle : 0.553 10.496 34671 Z= 0.276 Chirality : 0.047 0.346 4116 Planarity : 0.003 0.032 4416 Dihedral : 4.976 55.804 4560 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 11.92 % Favored : 86.53 % 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: 0.37 (0.15), residues: 3048 helix: 1.73 (0.21), residues: 696 sheet: 0.44 (0.18), residues: 663 loop : -0.44 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 104 HIS 0.002 0.001 HIS B1064 PHE 0.018 0.001 PHE C 464 TYR 0.040 0.001 TYR A 380 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 163 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7198 (tpt) cc_final: 0.6674 (tpp) REVERT: A 979 ASP cc_start: 0.7940 (t0) cc_final: 0.7664 (t0) REVERT: B 309 GLU cc_start: 0.7994 (mp0) cc_final: 0.7751 (mp0) REVERT: B 979 ASP cc_start: 0.7879 (t0) cc_final: 0.7442 (OUTLIER) REVERT: C 177 MET cc_start: 0.2574 (tpp) cc_final: 0.2275 (tmt) REVERT: C 979 ASP cc_start: 0.7898 (t0) cc_final: 0.7538 (t0) outliers start: 42 outliers final: 37 residues processed: 199 average time/residue: 1.1106 time to fit residues: 264.4930 Evaluate side-chains 191 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.0980 chunk 293 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 307 optimal weight: 0.0770 chunk 283 optimal weight: 0.8980 chunk 245 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 239 GLN B 957 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25494 Z= 0.190 Angle : 0.550 10.609 34671 Z= 0.275 Chirality : 0.047 0.345 4116 Planarity : 0.003 0.048 4416 Dihedral : 4.917 55.802 4560 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.52 % Allowed : 12.44 % Favored : 86.04 % 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: 0.37 (0.15), residues: 3048 helix: 1.76 (0.21), residues: 696 sheet: 0.47 (0.18), residues: 642 loop : -0.46 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 104 HIS 0.002 0.001 HIS B1064 PHE 0.028 0.001 PHE C 565 TYR 0.041 0.001 TYR A 380 ARG 0.011 0.000 ARG C 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7168 (tpt) cc_final: 0.6666 (tpp) REVERT: A 900 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8639 (mtm) REVERT: A 979 ASP cc_start: 0.7923 (t0) cc_final: 0.7645 (t0) REVERT: B 309 GLU cc_start: 0.7990 (mp0) cc_final: 0.7743 (mp0) REVERT: B 979 ASP cc_start: 0.7875 (t0) cc_final: 0.7438 (OUTLIER) REVERT: C 177 MET cc_start: 0.2617 (tpp) cc_final: 0.2301 (tmt) REVERT: C 408 ARG cc_start: 0.8730 (ttp80) cc_final: 0.8486 (tmm-80) REVERT: C 979 ASP cc_start: 0.7902 (t0) cc_final: 0.7537 (t0) outliers start: 41 outliers final: 39 residues processed: 196 average time/residue: 1.1455 time to fit residues: 270.7209 Evaluate side-chains 192 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 226 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.139271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087249 restraints weight = 42018.074| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.09 r_work: 0.2879 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 25494 Z= 0.355 Angle : 0.595 10.670 34671 Z= 0.297 Chirality : 0.048 0.344 4116 Planarity : 0.003 0.041 4416 Dihedral : 5.001 55.907 4560 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.67 % Allowed : 12.44 % Favored : 85.89 % 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: 0.25 (0.15), residues: 3048 helix: 1.62 (0.21), residues: 699 sheet: 0.45 (0.19), residues: 627 loop : -0.54 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 104 HIS 0.004 0.001 HIS B1064 PHE 0.033 0.001 PHE C 456 TYR 0.044 0.002 TYR A 380 ARG 0.010 0.001 ARG C 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6557.85 seconds wall clock time: 117 minutes 28.19 seconds (7048.19 seconds total)