Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 14:14:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/10_2023/6crv_7573.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/10_2023/6crv_7573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/10_2023/6crv_7573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/10_2023/6crv_7573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/10_2023/6crv_7573.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crv_7573/10_2023/6crv_7573.pdb" } resolution = 3.2 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= 0.008 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 13362 2.51 5 N 3438 2.21 5 O 4125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 21036 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 Chain: "B" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 Chain: "C" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 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 chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 11.38, per 1000 atoms: 0.54 Number of scatterers: 21036 At special positions: 0 Unit cell: (146.26, 149.35, 144.2, 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 4125 8.00 N 3438 7.00 C 13362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.00 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.00 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.00 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1304 " - " ASN A 691 " " NAG A1308 " - " ASN A1080 " " NAG A1309 " - " ASN A1116 " " NAG A1310 " - " ASN A1056 " " NAG A1311 " - " ASN A 602 " " NAG B1301 " - " ASN B 65 " " NAG B1304 " - " ASN B 691 " " NAG B1308 " - " ASN B1080 " " NAG B1309 " - " ASN B1116 " " NAG B1310 " - " ASN B1056 " " NAG B1311 " - " ASN B 602 " " NAG C1301 " - " ASN C 65 " " NAG C1304 " - " ASN C 691 " " NAG C1308 " - " ASN C1080 " " NAG C1309 " - " ASN C1116 " " NAG C1310 " - " ASN C1056 " " NAG C1311 " - " ASN C 602 " " NAG D 1 " - " ASN A 269 " " NAG E 1 " - " ASN A 783 " " NAG F 1 " - " ASN A 699 " " NAG G 1 " - " ASN B 269 " " NAG H 1 " - " ASN B 783 " " NAG I 1 " - " ASN B 699 " " NAG J 1 " - " ASN C 269 " " NAG K 1 " - " ASN C 783 " " NAG L 1 " - " ASN C 699 " Time building additional restraints: 8.78 Conformation dependent library (CDL) restraints added in 3.1 seconds 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 24.9% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 736 through 739 Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 763 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU A 803 " --> pdb=" O PHE A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE A 870 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.576A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.587A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.569A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 736 through 739 Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU B 803 " --> pdb=" O PHE B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE B 870 " --> pdb=" O GLY B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 890 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.576A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.588A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1013 removed outlier: 3.569A pdb=" N THR B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 736 through 739 Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 763 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU C 803 " --> pdb=" O PHE C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE C 870 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 895 through 900 removed outlier: 3.575A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.587A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1013 removed outlier: 3.568A pdb=" N THR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 998 " --> pdb=" O LEU C 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 35 removed outlier: 7.800A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS A 181 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE A 203 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG A 183 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN A 201 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE A 185 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY A 199 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE A 187 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR A 197 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN A 189 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 195 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.490A pdb=" N PHE A 47 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS A 133 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP A 154 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 removed outlier: 13.934A pdb=" N PHE A 231 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 13.118A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS A 133 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP A 154 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.952A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 314 removed outlier: 6.550A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL A 642 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.225A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A1041 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE A 782 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 823 Processing sheet with id=AB8, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.366A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 35 Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 35 removed outlier: 7.801A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS B 181 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE B 203 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG B 183 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN B 201 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE B 185 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY B 199 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE B 187 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR B 197 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASN B 189 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 195 " --> pdb=" O ASN B 189 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL B 123 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 164 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 125 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 162 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 127 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 129 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN B 158 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU B 131 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 156 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N CYS B 133 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP B 154 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 135 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 152 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 150 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 81 through 82 removed outlier: 13.934A pdb=" N PHE B 231 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 13.515A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 13.119A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 123 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 164 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 125 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 162 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 127 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 129 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN B 158 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU B 131 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 156 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N CYS B 133 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP B 154 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 135 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 152 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 150 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.952A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 312 through 314 removed outlier: 6.550A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL B 642 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.196A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B1041 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD3, first strand: chain 'B' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE B 782 " --> pdb=" O PHE B 779 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 821 through 823 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.366A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 31 through 35 Processing sheet with id=AD7, first strand: chain 'C' and resid 31 through 35 removed outlier: 7.801A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS C 181 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE C 203 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG C 183 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN C 201 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE C 185 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY C 199 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE C 187 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR C 197 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN C 189 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR C 195 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS C 133 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP C 154 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 81 through 82 removed outlier: 13.935A pdb=" N PHE C 231 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 13.119A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS C 133 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP C 154 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 615 through 616 removed outlier: 3.953A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C1041 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE7, first strand: chain 'C' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE C 782 " --> pdb=" O PHE C 779 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 821 through 823 Processing sheet with id=AE9, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.367A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.64 Time building geometry restraints manager: 9.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6362 1.33 - 1.46: 5223 1.46 - 1.58: 9742 1.58 - 1.71: 3 1.71 - 1.83: 153 Bond restraints: 21483 Sorted by residual: bond pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CB CYS C1014 " pdb=" SG CYS C1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CA TYR A 300 " pdb=" CB TYR A 300 " ideal model delta sigma weight residual 1.532 1.483 0.048 1.58e-02 4.01e+03 9.42e+00 bond pdb=" CA TYR C 300 " pdb=" CB TYR C 300 " ideal model delta sigma weight residual 1.532 1.484 0.048 1.58e-02 4.01e+03 9.38e+00 ... (remaining 21478 not shown) Histogram of bond angle deviations from ideal: 95.51 - 103.22: 201 103.22 - 110.93: 7925 110.93 - 118.64: 9013 118.64 - 126.35: 11829 126.35 - 134.06: 243 Bond angle restraints: 29211 Sorted by residual: angle pdb=" N GLY C 867 " pdb=" CA GLY C 867 " pdb=" C GLY C 867 " ideal model delta sigma weight residual 110.95 119.29 -8.34 1.70e+00 3.46e-01 2.40e+01 angle pdb=" N GLY B 867 " pdb=" CA GLY B 867 " pdb=" C GLY B 867 " ideal model delta sigma weight residual 110.95 119.27 -8.32 1.70e+00 3.46e-01 2.40e+01 angle pdb=" N GLY A 867 " pdb=" CA GLY A 867 " pdb=" C GLY A 867 " ideal model delta sigma weight residual 110.95 119.26 -8.31 1.70e+00 3.46e-01 2.39e+01 angle pdb=" C PHE C 83 " pdb=" N LYS C 84 " pdb=" CA LYS C 84 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C PHE A 83 " pdb=" N LYS A 84 " pdb=" CA LYS A 84 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 ... (remaining 29206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 12012 16.66 - 33.31: 384 33.31 - 49.96: 78 49.96 - 66.62: 9 66.62 - 83.27: 9 Dihedral angle restraints: 12492 sinusoidal: 4818 harmonic: 7674 Sorted by residual: dihedral pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " pdb=" SG CYS B1025 " pdb=" CB CYS B1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.27 83.27 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " pdb=" SG CYS A1025 " pdb=" CB CYS A1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.26 83.26 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS C1014 " pdb=" SG CYS C1014 " pdb=" SG CYS C1025 " pdb=" CB CYS C1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.25 83.25 1 1.00e+01 1.00e-02 8.47e+01 ... (remaining 12489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2221 0.057 - 0.115: 1021 0.115 - 0.172: 180 0.172 - 0.230: 31 0.230 - 0.287: 12 Chirality restraints: 3465 Sorted by residual: chirality pdb=" CB VAL A 711 " pdb=" CA VAL A 711 " pdb=" CG1 VAL A 711 " pdb=" CG2 VAL A 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL C 711 " pdb=" CA VAL C 711 " pdb=" CG1 VAL C 711 " pdb=" CG2 VAL C 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB VAL B 711 " pdb=" CA VAL B 711 " pdb=" CG1 VAL B 711 " pdb=" CG2 VAL B 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 3462 not shown) Planarity restraints: 3753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 868 " 0.017 2.00e-02 2.50e+03 1.95e-02 9.50e+00 pdb=" CG TRP B 868 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 868 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 868 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 868 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 868 " 0.017 2.00e-02 2.50e+03 1.94e-02 9.38e+00 pdb=" CG TRP A 868 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 868 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 868 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 868 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 868 " 0.017 2.00e-02 2.50e+03 1.93e-02 9.31e+00 pdb=" CG TRP C 868 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP C 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP C 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 868 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 868 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 868 " 0.005 2.00e-02 2.50e+03 ... (remaining 3750 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1339 2.72 - 3.26: 18996 3.26 - 3.81: 32848 3.81 - 4.35: 40034 4.35 - 4.90: 71121 Nonbonded interactions: 164338 Sorted by model distance: nonbonded pdb=" NH2 ARG A 306 " pdb=" OD1 ASP B 727 " model vdw 2.170 2.520 nonbonded pdb=" NH2 ARG B 306 " pdb=" OD1 ASP C 727 " model vdw 2.183 2.520 nonbonded pdb=" OE1 GLU B 999 " pdb=" NH2 ARG C1001 " model vdw 2.209 2.520 nonbonded pdb=" OE1 GLU A 999 " pdb=" NH2 ARG B1001 " model vdw 2.278 2.520 nonbonded pdb=" O GLY C 77 " pdb=" OH TYR C 252 " model vdw 2.302 2.440 ... (remaining 164333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.330 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 60.890 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.210 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.013 0.150 21483 Z= 0.834 Angle : 1.091 11.019 29211 Z= 0.597 Chirality : 0.064 0.287 3465 Planarity : 0.007 0.073 3726 Dihedral : 8.903 70.869 7443 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.26 % Allowed : 0.66 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -3.09 (0.13), residues: 2607 helix: -3.57 (0.10), residues: 600 sheet: -0.70 (0.19), residues: 642 loop : -1.98 (0.14), residues: 1365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 339 time to evaluate : 2.239 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 345 average time/residue: 0.3360 time to fit residues: 171.5402 Evaluate side-chains 177 residues out of total 2283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1411 time to fit residues: 2.8152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 239 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: