Starting phenix.real_space_refine on Fri Dec 15 09:16:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/12_2023/7s6k_24878.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/12_2023/7s6k_24878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/12_2023/7s6k_24878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/12_2023/7s6k_24878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/12_2023/7s6k_24878.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/12_2023/7s6k_24878.pdb" } resolution = 3.4 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= 0.036 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 144 5.16 5 C 19641 2.51 5 N 5100 2.21 5 O 6018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30903 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 5 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "B" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 5 Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "E" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 5 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 16.86, per 1000 atoms: 0.55 Number of scatterers: 30903 At special positions: 0 Unit cell: (151.8, 157.55, 205.85, 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 144 16.00 O 6018 8.00 N 5100 7.00 C 19641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS E 985 " distance=2.32 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS B 383 " distance=2.32 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B 985 " - pdb=" SG CYS E 383 " distance=2.32 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.01 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.04 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.01 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 17 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 17 " " NAG E1301 " - " ASN E 616 " " NAG E1302 " - " ASN E 709 " " NAG E1303 " - " ASN E 343 " " NAG E1304 " - " ASN E 61 " " NAG E1305 " - " ASN E 282 " " NAG E1306 " - " ASN E1074 " " NAG E1307 " - " ASN E 17 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN E 717 " " NAG S 1 " - " ASN E 801 " " NAG T 1 " - " ASN E1098 " " NAG U 1 " - " ASN E1134 " Time building additional restraints: 11.99 Conformation dependent library (CDL) restraints added in 5.7 seconds 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7242 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 63 sheets defined 20.5% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.875A 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 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.683A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.250A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.650A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'H' and resid 27 through 32 Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.875A 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 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.683A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.250A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.650A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 52A through 55 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.875A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.683A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.250A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 966 Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 3.650A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1147 Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 52A through 55 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.968A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.397A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.815A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.482A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.548A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.377A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.937A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.938A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU A 516 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.838A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.027A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.686A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.187A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.780A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.506A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR H 33 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.395A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.969A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASN B 196 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS B 202 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.397A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.816A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.482A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.550A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.377A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.937A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.938A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.837A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.027A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.687A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 788 through 790 removed outlier: 6.187A pdb=" N ILE B 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.780A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.505A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 33 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.394A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AE8, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.969A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN E 188 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE E 210 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG E 190 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR E 208 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE E 192 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS E 206 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE E 194 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR E 204 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASN E 196 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS E 202 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.398A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.815A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE E 140 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU E 156 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY E 142 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU E 154 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 83 through 85 removed outlier: 13.482A pdb=" N PHE E 238 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ASN E 137 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N THR E 240 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU E 242 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE E 140 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU E 156 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY E 142 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU E 154 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.550A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 324 through 326 removed outlier: 6.376A pdb=" N GLU E 324 " --> pdb=" O ASN E 540 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY E 566 " --> pdb=" O ASP E 574 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 348 through 349 removed outlier: 6.938A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.938A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU E 516 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL E 395 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER E 514 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA E 397 " --> pdb=" O VAL E 512 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL E 512 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER E 399 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL E 510 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL E 401 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR E 508 " --> pdb=" O VAL E 401 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.838A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN E1106 " --> pdb=" O GLU E1111 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU E1111 " --> pdb=" O GLN E1106 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 718 through 728 removed outlier: 6.028A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.687A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.780A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.506A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR F 33 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.395A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 13 1256 hydrogen bonds defined for protein. 3354 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: 20.14 Time building geometry restraints manager: 12.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5305 1.31 - 1.45: 10202 1.45 - 1.59: 15840 1.59 - 1.73: 87 1.73 - 1.87: 177 Bond restraints: 31611 Sorted by residual: bond pdb=" CB PHE F 100H" pdb=" CG PHE F 100H" ideal model delta sigma weight residual 1.502 1.352 0.150 2.30e-02 1.89e+03 4.28e+01 bond pdb=" CB PHE H 100H" pdb=" CG PHE H 100H" ideal model delta sigma weight residual 1.502 1.352 0.150 2.30e-02 1.89e+03 4.24e+01 bond pdb=" CB PHE C 100H" pdb=" CG PHE C 100H" ideal model delta sigma weight residual 1.502 1.353 0.149 2.30e-02 1.89e+03 4.19e+01 bond pdb=" CZ2 TRP A 152 " pdb=" CH2 TRP A 152 " ideal model delta sigma weight residual 1.368 1.490 -0.122 1.90e-02 2.77e+03 4.12e+01 bond pdb=" CZ2 TRP B 152 " pdb=" CH2 TRP B 152 " ideal model delta sigma weight residual 1.368 1.490 -0.122 1.90e-02 2.77e+03 4.10e+01 ... (remaining 31606 not shown) Histogram of bond angle deviations from ideal: 95.03 - 108.04: 2565 108.04 - 121.05: 31356 121.05 - 134.06: 9081 134.06 - 147.07: 9 147.07 - 160.08: 3 Bond angle restraints: 43014 Sorted by residual: angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 160.08 -35.52 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG R 1 " pdb=" N2 NAG R 1 " pdb=" C7 NAG R 1 " ideal model delta sigma weight residual 124.56 160.06 -35.50 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG N 1 " pdb=" N2 NAG N 1 " pdb=" C7 NAG N 1 " ideal model delta sigma weight residual 124.56 160.04 -35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N GLY A 261 " pdb=" CA GLY A 261 " pdb=" C GLY A 261 " ideal model delta sigma weight residual 112.14 100.54 11.60 1.29e+00 6.01e-01 8.09e+01 angle pdb=" N GLY E 261 " pdb=" CA GLY E 261 " pdb=" C GLY E 261 " ideal model delta sigma weight residual 112.14 100.54 11.60 1.29e+00 6.01e-01 8.08e+01 ... (remaining 43009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 18757 17.50 - 34.99: 476 34.99 - 52.49: 96 52.49 - 69.98: 84 69.98 - 87.48: 15 Dihedral angle restraints: 19428 sinusoidal: 8145 harmonic: 11283 Sorted by residual: dihedral pdb=" CB CYS B 985 " pdb=" SG CYS B 985 " pdb=" SG CYS E 383 " pdb=" CB CYS E 383 " ideal model delta sinusoidal sigma weight residual 93.00 19.08 73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 383 " pdb=" SG CYS A 383 " pdb=" SG CYS E 985 " pdb=" CB CYS E 985 " ideal model delta sinusoidal sigma weight residual 93.00 19.09 73.91 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 985 " pdb=" SG CYS A 985 " pdb=" SG CYS B 383 " pdb=" CB CYS B 383 " ideal model delta sinusoidal sigma weight residual 93.00 19.09 73.91 1 1.00e+01 1.00e-02 6.94e+01 ... (remaining 19425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3466 0.098 - 0.197: 1144 0.197 - 0.295: 226 0.295 - 0.394: 87 0.394 - 0.492: 60 Chirality restraints: 4983 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.41e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 4980 not shown) Planarity restraints: 5532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.075 2.00e-02 2.50e+03 8.14e-02 8.28e+01 pdb=" CG ASN A1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.132 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E1134 " 0.075 2.00e-02 2.50e+03 8.13e-02 8.26e+01 pdb=" CG ASN E1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN E1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E1134 " -0.131 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " 0.075 2.00e-02 2.50e+03 8.13e-02 8.25e+01 pdb=" CG ASN B1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " -0.131 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.096 2.00e-02 2.50e+03 ... (remaining 5529 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 12195 2.89 - 3.40: 28473 3.40 - 3.90: 53262 3.90 - 4.40: 61444 4.40 - 4.90: 99552 Nonbonded interactions: 254926 Sorted by model distance: nonbonded pdb=" N TYR B 351 " pdb=" N ALA B 352 " model vdw 2.392 2.560 nonbonded pdb=" N TYR E 351 " pdb=" N ALA E 352 " model vdw 2.393 2.560 nonbonded pdb=" N TYR A 351 " pdb=" N ALA A 352 " model vdw 2.393 2.560 nonbonded pdb=" NZ LYS B 854 " pdb=" OD2 ASP E 614 " model vdw 2.395 2.520 nonbonded pdb=" NZ LYS A 854 " pdb=" OD2 ASP B 614 " model vdw 2.395 2.520 ... (remaining 254921 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 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.560 Check model and map are aligned: 0.520 Set scattering table: 0.290 Process input model: 91.160 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: