Starting phenix.real_space_refine on Sat Aug 10 12:14:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/08_2024/7xoa_33342.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/08_2024/7xoa_33342.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/7xoa_33342/08_2024/7xoa_33342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/08_2024/7xoa_33342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/08_2024/7xoa_33342.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/08_2024/7xoa_33342.cif" } 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= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 134 5.16 5 C 18667 2.51 5 N 4812 2.21 5 O 5588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D ARG 600": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29202 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 7950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7950 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 7950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7950 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 17.41, per 1000 atoms: 0.60 Number of scatterers: 29202 At special positions: 0 Unit cell: (132.664, 136.784, 246.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 134 16.00 O 5588 8.00 N 4812 7.00 C 18667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, 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=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.32 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.98 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.99 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.60 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 B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.76 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 331 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 801 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 122 " " NAG C1310 " - " ASN C 331 " " NAG C1311 " - " ASN C 709 " " NAG D 902 " - " ASN D 546 " " NAG D 903 " - " ASN D 53 " Time building additional restraints: 12.81 Conformation dependent library (CDL) restraints added in 6.7 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 49 sheets defined 30.4% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.633A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.188A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.503A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 778 removed outlier: 4.029A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.508A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.787A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.109A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.146A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.702A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.327A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.595A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.818A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 778 removed outlier: 3.841A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.533A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.782A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.120A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.541A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.958A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.536A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.672A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.533A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.560A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.548A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 778 removed outlier: 3.690A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 868 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.556A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.779A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.137A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.152A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.524A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1033 removed outlier: 3.581A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.781A pdb=" N ASN D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.808A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.798A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.147A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.732A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.734A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 4.375A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 removed outlier: 4.204A pdb=" N ILE D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.579A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.528A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.540A pdb=" N ALA D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.649A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.153A pdb=" N ARG D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.824A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.747A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.656A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.557A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.569A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.615A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.062A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.817A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 172 removed outlier: 3.985A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.622A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.599A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.685A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.116A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.212A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.856A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.810A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.837A 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 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.525A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.198A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.048A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 126 through 132 removed outlier: 3.550A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 316 removed outlier: 5.319A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.113A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.513A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.527A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.710A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 714 removed outlier: 3.809A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.831A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.293A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.526A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.515A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.099A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.646A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.913A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.299A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.911A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.508A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.549A pdb=" N TYR C 453 " --> pdb=" O ARG C 493 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 538 through 539 removed outlier: 3.534A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.742A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.621A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.832A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.811A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.185A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.566A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.738A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 350 1111 hydrogen bonds defined for protein. 3033 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: 18.10 Time building geometry restraints manager: 14.15 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: 6036 1.33 - 1.45: 7355 1.45 - 1.57: 16336 1.57 - 1.70: 0 1.70 - 1.82: 179 Bond restraints: 29906 Sorted by residual: bond pdb=" CA ALA C 292 " pdb=" CB ALA C 292 " ideal model delta sigma weight residual 1.527 1.497 0.031 7.60e-03 1.73e+04 1.64e+01 bond pdb=" N VAL C 289 " pdb=" CA VAL C 289 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ASP A 294 " pdb=" CA ASP A 294 " ideal model delta sigma weight residual 1.455 1.474 -0.019 7.00e-03 2.04e+04 7.61e+00 bond pdb=" N HIS B 519 " pdb=" CA HIS B 519 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.49e+00 bond pdb=" CA ALA A 288 " pdb=" CB ALA A 288 " ideal model delta sigma weight residual 1.535 1.483 0.052 1.90e-02 2.77e+03 7.46e+00 ... (remaining 29901 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 976 107.01 - 113.76: 16289 113.76 - 120.50: 11375 120.50 - 127.25: 11771 127.25 - 133.99: 297 Bond angle restraints: 40708 Sorted by residual: angle pdb=" CA PHE A 374 " pdb=" CB PHE A 374 " pdb=" CG PHE A 374 " ideal model delta sigma weight residual 113.80 120.48 -6.68 1.00e+00 1.00e+00 4.46e+01 angle pdb=" CA PHE A 371 " pdb=" C PHE A 371 " pdb=" O PHE A 371 " ideal model delta sigma weight residual 121.46 114.57 6.89 1.17e+00 7.31e-01 3.47e+01 angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 118.44 127.21 -8.77 1.59e+00 3.96e-01 3.04e+01 angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" O ALA B 520 " ideal model delta sigma weight residual 120.16 112.61 7.55 1.37e+00 5.33e-01 3.04e+01 angle pdb=" O ASP A 287 " pdb=" C ASP A 287 " pdb=" N ALA A 288 " ideal model delta sigma weight residual 123.48 117.24 6.24 1.14e+00 7.69e-01 3.00e+01 ... (remaining 40703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 17786 23.03 - 46.05: 330 46.05 - 69.08: 32 69.08 - 92.10: 19 92.10 - 115.13: 17 Dihedral angle restraints: 18184 sinusoidal: 7482 harmonic: 10702 Sorted by residual: dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -160.06 74.06 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -150.16 64.16 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -142.36 56.36 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 18181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4055 0.062 - 0.124: 560 0.124 - 0.186: 26 0.186 - 0.248: 12 0.248 - 0.310: 6 Chirality restraints: 4659 Sorted by residual: chirality pdb=" CA PHE A 371 " pdb=" N PHE A 371 " pdb=" C PHE A 371 " pdb=" CB PHE A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ALA B 292 " pdb=" N ALA B 292 " pdb=" C ALA B 292 " pdb=" CB ALA B 292 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA CYS B 131 " pdb=" N CYS B 131 " pdb=" C CYS B 131 " pdb=" CB CYS B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 4656 not shown) Planarity restraints: 5252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1311 " 0.306 2.00e-02 2.50e+03 2.58e-01 8.32e+02 pdb=" C7 NAG C1311 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C1311 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C1311 " -0.443 2.00e-02 2.50e+03 pdb=" O7 NAG C1311 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 366 " -0.023 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C SER A 366 " 0.078 2.00e-02 2.50e+03 pdb=" O SER A 366 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL A 367 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 288 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C ALA C 288 " -0.054 2.00e-02 2.50e+03 pdb=" O ALA C 288 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL C 289 " 0.018 2.00e-02 2.50e+03 ... (remaining 5249 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 111 2.47 - 3.08: 19550 3.08 - 3.69: 42209 3.69 - 4.29: 62475 4.29 - 4.90: 104598 Nonbonded interactions: 228943 Sorted by model distance: nonbonded pdb=" O CYS B 391 " pdb=" NE2 HIS B 519 " model vdw 1.863 3.120 nonbonded pdb=" NH1 ARG C 577 " pdb=" CD1 LEU C 582 " model vdw 1.900 3.540 nonbonded pdb=" CZ PHE B 375 " pdb=" CE2 TYR B 508 " model vdw 2.058 3.640 nonbonded pdb=" SG CYS B 336 " pdb=" O VAL B 362 " model vdw 2.067 3.400 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.170 3.040 ... (remaining 228938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 426 or (resid 427 and (name N or name CA or name C or name O or nam \ e CB )) or resid 428 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 and (name N or name CA or name C or name O or name CB )) or resid 460 \ through 464 or (resid 465 and (name N or name CA or name C or name O or name CB \ )) or resid 466 through 473 or (resid 474 through 475 and (name N or name CA or \ name C or name O or name CB )) or resid 476 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 522 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 1146 or resid 1301 through 1310)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 1146 or resid 1301 through 1310)) } 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: 7.830 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: 0.030 Extract box with map and model: 1.150 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 101.060 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.160 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4609 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 : 0.003 0.053 29906 Z= 0.180 Angle : 0.565 9.543 40708 Z= 0.336 Chirality : 0.044 0.310 4659 Planarity : 0.005 0.258 5219 Dihedral : 9.797 115.126 11200 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.12), residues: 3618 helix: -0.33 (0.16), residues: 1009 sheet: -1.39 (0.18), residues: 594 loop : -2.76 (0.11), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.002 0.000 HIS B 519 PHE 0.031 0.001 PHE A 374 TYR 0.010 0.001 TYR A 265 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 693 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 TYR cc_start: 0.7093 (m-80) cc_final: 0.6783 (m-80) REVERT: A 595 VAL cc_start: 0.8339 (m) cc_final: 0.8052 (t) REVERT: A 698 SER cc_start: 0.8489 (t) cc_final: 0.8222 (p) REVERT: A 737 ASP cc_start: 0.6712 (t70) cc_final: 0.6393 (t0) REVERT: A 821 LEU cc_start: 0.8349 (tt) cc_final: 0.8079 (tp) REVERT: A 822 LEU cc_start: 0.7926 (mt) cc_final: 0.7654 (mp) REVERT: A 875 SER cc_start: 0.8408 (t) cc_final: 0.7922 (m) REVERT: A 881 THR cc_start: 0.7849 (t) cc_final: 0.7628 (t) REVERT: A 929 SER cc_start: 0.8070 (t) cc_final: 0.7828 (p) REVERT: A 1002 GLN cc_start: 0.7169 (tt0) cc_final: 0.6939 (tt0) REVERT: B 290 ASP cc_start: 0.7514 (t0) cc_final: 0.7260 (t0) REVERT: B 340 GLU cc_start: 0.6294 (tp30) cc_final: 0.6035 (tp30) REVERT: B 354 ASN cc_start: 0.7342 (m-40) cc_final: 0.6914 (m-40) REVERT: B 398 ASP cc_start: 0.6368 (m-30) cc_final: 0.6061 (m-30) REVERT: B 420 ASP cc_start: 0.6550 (m-30) cc_final: 0.6325 (m-30) REVERT: B 494 SER cc_start: 0.7248 (m) cc_final: 0.6918 (t) REVERT: B 513 LEU cc_start: 0.7845 (mt) cc_final: 0.7414 (mp) REVERT: B 663 ASP cc_start: 0.6974 (p0) cc_final: 0.6699 (p0) REVERT: B 864 LEU cc_start: 0.7792 (tp) cc_final: 0.7442 (tp) REVERT: B 905 ARG cc_start: 0.6905 (mtt-85) cc_final: 0.6701 (mtp85) REVERT: B 1017 GLU cc_start: 0.6604 (tp30) cc_final: 0.5980 (tp30) REVERT: B 1084 ASP cc_start: 0.6946 (t0) cc_final: 0.6394 (t0) REVERT: B 1123 SER cc_start: 0.7979 (t) cc_final: 0.7694 (t) REVERT: C 45 SER cc_start: 0.8024 (p) cc_final: 0.7740 (p) REVERT: C 303 LEU cc_start: 0.8484 (tp) cc_final: 0.8168 (tt) REVERT: C 305 SER cc_start: 0.8409 (m) cc_final: 0.8184 (m) REVERT: C 595 VAL cc_start: 0.8225 (m) cc_final: 0.7920 (t) REVERT: C 774 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7271 (mm110) REVERT: C 800 PHE cc_start: 0.7373 (m-80) cc_final: 0.5535 (m-80) REVERT: C 822 LEU cc_start: 0.7633 (mt) cc_final: 0.7432 (mt) REVERT: C 907 ASN cc_start: 0.7266 (t0) cc_final: 0.6856 (t0) REVERT: C 1038 LYS cc_start: 0.7764 (mmmm) cc_final: 0.7544 (mmmm) REVERT: D 499 ASP cc_start: -0.1173 (m-30) cc_final: -0.2538 (p0) REVERT: D 557 MET cc_start: -0.1026 (tmm) cc_final: -0.1288 (tmm) outliers start: 2 outliers final: 2 residues processed: 695 average time/residue: 0.3979 time to fit residues: 435.0610 Evaluate side-chains 519 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 517 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 374 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 8.9990 chunk 276 optimal weight: 0.5980 chunk 153 optimal weight: 0.0020 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 286 optimal weight: 0.0040 chunk 110 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 331 optimal weight: 2.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 173 GLN A 394 ASN A 414 GLN A 505 HIS A 540 ASN A 563 GLN A 607 GLN A 755 GLN A 774 GLN A 784 GLN A 804 GLN A 935 GLN A 955 ASN A 965 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 52 GLN B 81 ASN B 282 ASN B 394 ASN B 613 GLN B 907 ASN B 965 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 173 GLN C 196 ASN C 606 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 907 ASN C1010 GLN C1023 ASN C1106 GLN D 42 GLN D 60 GLN D 86 GLN D 98 GLN D 221 GLN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN D 345 HIS D 368 ASN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN D 472 GLN D 522 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4893 moved from start: 0.2233 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: