Starting phenix.real_space_refine on Fri Jul 26 17:13:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc0_39918/07_2024/8zc0_39918.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc0_39918/07_2024/8zc0_39918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc0_39918/07_2024/8zc0_39918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc0_39918/07_2024/8zc0_39918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc0_39918/07_2024/8zc0_39918.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc0_39918/07_2024/8zc0_39918.cif" } resolution = 4.17 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= 0.002 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 21633 2.51 5 N 5566 2.21 5 O 6632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1139": "OD1" <-> "OD2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 53": "OD1" <-> "OD2" Residue "N TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 57": "OD1" <-> "OD2" Residue "R ASP 57": "OD1" <-> "OD2" Residue "R ASP 90": "OD1" <-> "OD2" Residue "R ASP 115": "OD1" <-> "OD2" Time to flip residues: 0.58s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 33975 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7793 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "B" Number of atoms: 7793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7793 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "C" Number of atoms: 7781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7781 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 10 Chain: "G" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "H" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "M" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "N" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "Q" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.90, per 1000 atoms: 0.50 Number of scatterers: 33975 At special positions: 0 Unit cell: (176.88, 207.24, 240.24, 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 6632 8.00 N 5566 7.00 C 21633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 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=2.03 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 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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 G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 145 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 145 " - pdb=" SG CYS M 204 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 204 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 103 " - pdb=" SG CYS Q 108 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 154 " - pdb=" SG CYS Q 210 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 108 " distance=2.03 Simple disulfide: pdb=" SG CYS R 154 " - pdb=" SG CYS R 210 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 657 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 234 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN A 331 " " NAG L 1 " - " ASN B 709 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 331 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN C 616 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 12.58 Conformation dependent library (CDL) restraints added in 5.8 seconds 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8002 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 77 sheets defined 17.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.04 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 383 through 387 removed outlier: 3.513A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.763A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.802A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 781 removed outlier: 3.571A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.783A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.442A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.778A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.921A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.225A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) 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 removed outlier: 4.048A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.944A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.503A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.762A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.506A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.536A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.767A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.573A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.675A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.187A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.866A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.631A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.290A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.038A pdb=" N GLU G 84 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 139 Processing helix chain 'G' and resid 192 through 197 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.787A pdb=" N ARG H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 138 removed outlier: 3.629A pdb=" N LEU M 136 " --> pdb=" O SER M 132 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA M 138 " --> pdb=" O GLU M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 197 Processing helix chain 'N' and resid 132 through 138 Processing helix chain 'N' and resid 192 through 199 removed outlier: 3.699A pdb=" N TRP N 196 " --> pdb=" O THR N 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.556A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 3.829A pdb=" N ASP R 90 " --> pdb=" O ARG R 87 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR R 91 " --> pdb=" O SER R 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 87 through 91' Processing helix chain 'R' and resid 106 through 112 removed outlier: 3.682A pdb=" N GLN R 109 " --> pdb=" O ASN R 106 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG R 110 " --> pdb=" O SER R 107 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP R 111 " --> pdb=" O CYS R 108 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET R 112 " --> pdb=" O GLN R 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 106 through 112' Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.744A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.744A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.739A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.394A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.605A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 435 " --> pdb=" O ALA A 376 " (cutoff:3.500A) 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: 3.866A 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: 3.698A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.353A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 727 removed outlier: 3.726A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.525A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.784A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.267A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.725A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.644A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.556A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.541A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.033A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.608A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.625A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.607A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.912A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 286 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.721A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.519A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.620A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.511A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.153A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.445A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.951A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.538A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.908A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.754A pdb=" N THR G 108 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 19 through 23 Processing sheet with id=AF3, first strand: chain 'G' and resid 45 through 49 removed outlier: 7.009A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR G 37 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP G 93 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY G 98 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.582A pdb=" N SER G 125 " --> pdb=" O SER G 148 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER G 148 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR G 127 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 146 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE G 129 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL G 144 " --> pdb=" O PHE G 129 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 143 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS G 145 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP G 149 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR G 183 " --> pdb=" O ASP G 149 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.582A pdb=" N SER G 125 " --> pdb=" O SER G 148 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER G 148 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR G 127 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 146 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE G 129 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL G 144 " --> pdb=" O PHE G 129 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 143 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS G 145 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP G 149 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR G 183 " --> pdb=" O ASP G 149 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA G 184 " --> pdb=" O SER G 176 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER G 176 " --> pdb=" O ALA G 184 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 157 through 160 Processing sheet with id=AF7, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.578A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS H 22 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 32 through 39 Processing sheet with id=AF9, first strand: chain 'H' and resid 32 through 39 removed outlier: 3.509A pdb=" N ALA H 121 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 49 through 51 removed outlier: 4.035A pdb=" N TRP H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'H' and resid 151 through 159 removed outlier: 3.564A pdb=" N CYS H 154 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER H 194 " --> pdb=" O CYS H 154 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU H 192 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP H 158 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 164 through 168 removed outlier: 3.692A pdb=" N THR H 165 " --> pdb=" O ASN H 213 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN H 213 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS H 210 " --> pdb=" O LYS H 223 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AG5, first strand: chain 'M' and resid 18 through 22 removed outlier: 3.665A pdb=" N ALA M 72 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 45 through 49 removed outlier: 6.953A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN M 39 " --> pdb=" O ASP M 86 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL M 100 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP M 93 " --> pdb=" O GLY M 98 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 125 through 129 removed outlier: 3.899A pdb=" N VAL M 144 " --> pdb=" O PHE M 129 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP M 149 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR M 183 " --> pdb=" O ASP M 149 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR M 188 " --> pdb=" O GLU M 171 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU M 171 " --> pdb=" O TYR M 188 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 125 through 129 removed outlier: 3.899A pdb=" N VAL M 144 " --> pdb=" O PHE M 129 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP M 149 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR M 183 " --> pdb=" O ASP M 149 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 157 through 160 Processing sheet with id=AH1, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.654A pdb=" N VAL N 18 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE N 76 " --> pdb=" O VAL N 18 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 45 through 49 removed outlier: 6.649A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN N 39 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA N 91 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL N 100 " --> pdb=" O ALA N 91 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 45 through 49 removed outlier: 6.649A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN N 39 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 125 through 128 removed outlier: 3.755A pdb=" N SER N 148 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR N 127 " --> pdb=" O LEU N 146 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU N 146 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA N 141 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS N 145 " --> pdb=" O SER N 187 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER N 187 " --> pdb=" O CYS N 145 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 125 through 128 removed outlier: 3.755A pdb=" N SER N 148 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR N 127 " --> pdb=" O LEU N 146 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU N 146 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR N 183 " --> pdb=" O ASP N 149 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 45 through 46 removed outlier: 4.196A pdb=" N GLU Q 46 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG Q 38 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 45 through 46 removed outlier: 4.196A pdb=" N GLU Q 46 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG Q 38 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL Q 37 " --> pdb=" O PHE Q 95 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL Q 93 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL Q 123 " --> pdb=" O ALA Q 92 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 68 through 71 Processing sheet with id=AH9, first strand: chain 'Q' and resid 150 through 155 removed outlier: 3.798A pdb=" N CYS Q 154 " --> pdb=" O SER Q 194 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER Q 194 " --> pdb=" O CYS Q 154 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 165 through 168 removed outlier: 4.271A pdb=" N THR Q 165 " --> pdb=" O ASN Q 213 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN Q 213 " --> pdb=" O THR Q 165 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS Q 223 " --> pdb=" O CYS Q 210 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL Q 212 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 6 through 7 removed outlier: 3.783A pdb=" N SER R 21 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP R 73 " --> pdb=" O THR R 78 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU R 82 " --> pdb=" O THR R 69 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR R 69 " --> pdb=" O GLU R 82 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 58 through 60 removed outlier: 3.504A pdb=" N TRP R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL R 37 " --> pdb=" O PHE R 95 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 134 through 136 removed outlier: 3.615A pdb=" N LEU R 155 " --> pdb=" O PHE R 136 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR R 190 " --> pdb=" O ASP R 158 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER R 191 " --> pdb=" O VAL R 183 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'R' and resid 165 through 168 removed outlier: 4.004A pdb=" N VAL R 212 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL R 221 " --> pdb=" O VAL R 212 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS R 214 " --> pdb=" O THR R 219 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR R 219 " --> pdb=" O HIS R 214 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 2823 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: 15.16 Time building geometry restraints manager: 13.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10711 1.35 - 1.47: 9039 1.47 - 1.60: 14849 1.60 - 1.72: 0 1.72 - 1.85: 180 Bond restraints: 34779 Sorted by residual: bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.23e+00 ... (remaining 34774 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.67: 876 105.67 - 112.77: 18622 112.77 - 119.88: 10954 119.88 - 126.98: 16489 126.98 - 134.08: 411 Bond angle restraints: 47352 Sorted by residual: angle pdb=" N ASP R 56 " pdb=" CA ASP R 56 " pdb=" C ASP R 56 " ideal model delta sigma weight residual 112.93 107.59 5.34 1.12e+00 7.97e-01 2.27e+01 angle pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" C ASN B 360 " ideal model delta sigma weight residual 112.24 117.56 -5.32 1.28e+00 6.10e-01 1.73e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.09 -4.39 1.22e+00 6.72e-01 1.29e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.06 -4.36 1.22e+00 6.72e-01 1.28e+01 angle pdb=" C LYS R 157 " pdb=" N ASP R 158 " pdb=" CA ASP R 158 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 ... (remaining 47347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19474 18.00 - 36.00: 1612 36.00 - 54.00: 275 54.00 - 72.00: 62 72.00 - 90.00: 39 Dihedral angle restraints: 21462 sinusoidal: 9030 harmonic: 12432 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 5.35 87.65 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 10.51 82.49 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -6.84 -79.16 1 1.00e+01 1.00e-02 7.79e+01 ... (remaining 21459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 5474 0.135 - 0.270: 45 0.270 - 0.405: 2 0.405 - 0.540: 0 0.540 - 0.675: 1 Chirality restraints: 5522 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.81e+02 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 5519 not shown) Planarity restraints: 6049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG L 2 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.129 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.243 2.00e-02 2.50e+03 2.07e-01 5.35e+02 pdb=" C7 NAG L 1 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.342 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 294 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO B 295 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " 0.036 5.00e-02 4.00e+02 ... (remaining 6046 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5337 2.77 - 3.30: 29610 3.30 - 3.83: 54305 3.83 - 4.37: 57305 4.37 - 4.90: 104019 Nonbonded interactions: 250576 Sorted by model distance: nonbonded pdb=" O PRO C 85 " pdb=" OH TYR C 269 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.261 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.269 2.440 nonbonded pdb=" OE2 GLU H 46 " pdb=" OG SER H 63 " model vdw 2.276 2.440 nonbonded pdb=" O ASN Q 33 " pdb=" OG SER Q 99 " model vdw 2.285 2.440 ... (remaining 250571 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' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1147 or resid 1301 through 1306)) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1147 or resid 1301 through 1306)) selection = (chain 'C' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.760 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: 1.470 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 87.570 Find NCS groups from input model: 4.560 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 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 : 0.004 0.048 34779 Z= 0.232 Angle : 0.687 9.300 47352 Z= 0.356 Chirality : 0.050 0.675 5522 Planarity : 0.007 0.295 6010 Dihedral : 13.628 89.999 13307 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 0.11 % Allowed : 0.51 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.48 (0.12), residues: 4193 helix: 0.19 (0.20), residues: 653 sheet: -0.35 (0.17), residues: 929 loop : -1.60 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 50 HIS 0.018 0.001 HIS A 954 PHE 0.030 0.001 PHE C 374 TYR 0.036 0.001 TYR N 50 ARG 0.010 0.000 ARG N 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 222 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8171 (mtm) cc_final: 0.7875 (mtm) REVERT: A 1118 ASP cc_start: 0.7161 (p0) cc_final: 0.6946 (p0) REVERT: C 731 MET cc_start: 0.8998 (pmm) cc_final: 0.8714 (pmm) REVERT: N 16 GLN cc_start: 0.6009 (pp30) cc_final: 0.5806 (pt0) REVERT: Q 113 TRP cc_start: 0.5475 (p-90) cc_final: 0.5256 (p-90) REVERT: R 73 ASP cc_start: 0.5194 (m-30) cc_final: 0.4351 (m-30) REVERT: R 112 MET cc_start: 0.8392 (mmp) cc_final: 0.7960 (mmm) outliers start: 4 outliers final: 2 residues processed: 225 average time/residue: 0.4237 time to fit residues: 164.6653 Evaluate side-chains 142 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 386 optimal weight: 0.2980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1142 GLN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34779 Z= 0.213 Angle : 0.536 9.792 47352 Z= 0.277 Chirality : 0.044 0.395 5522 Planarity : 0.004 0.059 6010 Dihedral : 5.839 59.829 5761 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.05 % Allowed : 4.52 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.03 (0.13), residues: 4193 helix: 1.20 (0.21), residues: 643 sheet: -0.16 (0.17), residues: 963 loop : -1.45 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 50 HIS 0.006 0.001 HIS A 954 PHE 0.028 0.001 PHE A 275 TYR 0.022 0.001 TYR B1067 ARG 0.003 0.000 ARG N 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9305 (m) cc_final: 0.8893 (p) REVERT: A 1118 ASP cc_start: 0.7343 (p0) cc_final: 0.7133 (p0) REVERT: B 1029 MET cc_start: 0.9023 (tpp) cc_final: 0.8756 (tpp) REVERT: C 731 MET cc_start: 0.9109 (pmm) cc_final: 0.8608 (pmm) REVERT: G 46 LYS cc_start: 0.2838 (mppt) cc_final: 0.2511 (tptm) REVERT: N 16 GLN cc_start: 0.6355 (pp30) cc_final: 0.5920 (pt0) outliers start: 2 outliers final: 2 residues processed: 206 average time/residue: 0.4127 time to fit residues: 146.9558 Evaluate side-chains 133 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 6.9990 chunk 120 optimal weight: 0.5980 chunk 321 optimal weight: 20.0000 chunk 263 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 387 optimal weight: 0.6980 chunk 418 optimal weight: 9.9990 chunk 345 optimal weight: 8.9990 chunk 384 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1106 GLN B 207 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN R 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34779 Z= 0.232 Angle : 0.536 7.937 47352 Z= 0.273 Chirality : 0.044 0.384 5522 Planarity : 0.004 0.058 6010 Dihedral : 5.381 59.769 5761 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 4193 helix: 1.45 (0.22), residues: 647 sheet: -0.19 (0.17), residues: 973 loop : -1.39 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Q 50 HIS 0.005 0.001 HIS A 954 PHE 0.022 0.001 PHE C 238 TYR 0.021 0.001 TYR B1067 ARG 0.003 0.000 ARG Q 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9322 (m) cc_final: 0.8954 (p) REVERT: B 1029 MET cc_start: 0.8980 (tpp) cc_final: 0.8742 (tpp) REVERT: C 610 VAL cc_start: 0.9634 (t) cc_final: 0.9409 (m) REVERT: C 987 PRO cc_start: 0.7680 (Cg_exo) cc_final: 0.6998 (Cg_endo) REVERT: G 46 LYS cc_start: 0.3308 (mppt) cc_final: 0.2902 (tptm) REVERT: R 119 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7462 (pp30) outliers start: 2 outliers final: 1 residues processed: 225 average time/residue: 0.4159 time to fit residues: 160.2131 Evaluate side-chains 140 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 3.9990 chunk 291 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 411 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 368 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 43 GLN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34779 Z= 0.295 Angle : 0.571 7.328 47352 Z= 0.291 Chirality : 0.045 0.367 5522 Planarity : 0.004 0.048 6010 Dihedral : 5.229 58.558 5761 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4193 helix: 1.47 (0.21), residues: 641 sheet: -0.30 (0.16), residues: 986 loop : -1.42 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 50 HIS 0.004 0.001 HIS A 954 PHE 0.026 0.002 PHE C 275 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 4.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9349 (m) cc_final: 0.8997 (p) REVERT: A 731 MET cc_start: 0.9195 (ppp) cc_final: 0.7955 (ppp) REVERT: C 987 PRO cc_start: 0.7792 (Cg_exo) cc_final: 0.7012 (Cg_endo) REVERT: H 114 PHE cc_start: 0.3959 (m-10) cc_final: 0.3466 (m-10) outliers start: 1 outliers final: 1 residues processed: 201 average time/residue: 0.4307 time to fit residues: 150.8517 Evaluate side-chains 129 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 306 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 351 optimal weight: 0.8980 chunk 284 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 210 optimal weight: 0.0980 chunk 369 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN H 3 GLN ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34779 Z= 0.206 Angle : 0.525 7.784 47352 Z= 0.266 Chirality : 0.044 0.366 5522 Planarity : 0.004 0.050 6010 Dihedral : 5.007 56.665 5761 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 4193 helix: 1.55 (0.22), residues: 650 sheet: -0.28 (0.16), residues: 978 loop : -1.38 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 50 HIS 0.005 0.001 HIS B 954 PHE 0.024 0.001 PHE C 429 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG R 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9325 (m) cc_final: 0.9009 (p) REVERT: A 962 LEU cc_start: 0.9385 (tp) cc_final: 0.9139 (tt) REVERT: C 987 PRO cc_start: 0.7777 (Cg_exo) cc_final: 0.7027 (Cg_endo) REVERT: H 114 PHE cc_start: 0.3980 (m-10) cc_final: 0.3439 (m-10) REVERT: R 90 ASP cc_start: 0.6873 (m-30) cc_final: 0.6571 (m-30) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.4215 time to fit residues: 156.4356 Evaluate side-chains 132 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 6.9990 chunk 370 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 101 optimal weight: 0.2980 chunk 412 optimal weight: 10.0000 chunk 342 optimal weight: 0.1980 chunk 190 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN H 43 GLN ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34779 Z= 0.222 Angle : 0.533 8.515 47352 Z= 0.269 Chirality : 0.044 0.358 5522 Planarity : 0.004 0.056 6010 Dihedral : 4.896 54.428 5761 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 4193 helix: 1.52 (0.22), residues: 655 sheet: -0.32 (0.17), residues: 992 loop : -1.33 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 50 HIS 0.004 0.001 HIS A 245 PHE 0.026 0.001 PHE C 429 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG N 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9319 (m) cc_final: 0.9009 (p) REVERT: B 1029 MET cc_start: 0.8980 (tpp) cc_final: 0.8719 (tpp) REVERT: H 114 PHE cc_start: 0.3684 (m-10) cc_final: 0.3133 (m-10) REVERT: Q 28 ILE cc_start: 0.8764 (tp) cc_final: 0.8504 (tp) REVERT: R 6 GLN cc_start: 0.7731 (pt0) cc_final: 0.7362 (pp30) REVERT: R 90 ASP cc_start: 0.6836 (m-30) cc_final: 0.6551 (m-30) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.3998 time to fit residues: 147.8956 Evaluate side-chains 140 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 300 optimal weight: 0.2980 chunk 233 optimal weight: 2.9990 chunk 346 optimal weight: 20.0000 chunk 230 optimal weight: 5.9990 chunk 410 optimal weight: 0.0030 chunk 256 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34779 Z= 0.176 Angle : 0.511 8.791 47352 Z= 0.258 Chirality : 0.043 0.354 5522 Planarity : 0.004 0.050 6010 Dihedral : 4.721 50.066 5761 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4193 helix: 1.67 (0.22), residues: 649 sheet: -0.22 (0.17), residues: 977 loop : -1.31 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 113 HIS 0.002 0.000 HIS C1048 PHE 0.016 0.001 PHE Q 29 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG Q 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9300 (m) cc_final: 0.8991 (p) REVERT: A 962 LEU cc_start: 0.9374 (tp) cc_final: 0.9134 (tt) REVERT: B 786 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7707 (mmtm) REVERT: C 223 LEU cc_start: 0.7984 (mm) cc_final: 0.7769 (mm) REVERT: N 5 THR cc_start: 0.8515 (p) cc_final: 0.8306 (p) REVERT: R 6 GLN cc_start: 0.7625 (pt0) cc_final: 0.7287 (pp30) REVERT: R 90 ASP cc_start: 0.6863 (m-30) cc_final: 0.6472 (m-30) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.4051 time to fit residues: 149.6051 Evaluate side-chains 138 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN G 52 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34779 Z= 0.208 Angle : 0.530 8.866 47352 Z= 0.267 Chirality : 0.044 0.353 5522 Planarity : 0.004 0.057 6010 Dihedral : 4.688 49.178 5761 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4193 helix: 1.66 (0.22), residues: 651 sheet: -0.24 (0.17), residues: 980 loop : -1.32 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 36 HIS 0.002 0.001 HIS H 35 PHE 0.027 0.001 PHE C 238 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9284 (m) cc_final: 0.9013 (p) REVERT: A 731 MET cc_start: 0.8991 (ppp) cc_final: 0.8372 (ppp) REVERT: A 962 LEU cc_start: 0.9397 (tp) cc_final: 0.9153 (tt) REVERT: B 786 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7717 (mmtm) REVERT: C 223 LEU cc_start: 0.8022 (mm) cc_final: 0.7792 (mm) REVERT: R 80 TYR cc_start: 0.6742 (m-10) cc_final: 0.6510 (m-10) REVERT: R 90 ASP cc_start: 0.6767 (m-30) cc_final: 0.6428 (m-30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.3954 time to fit residues: 144.0407 Evaluate side-chains 138 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 0.9980 chunk 393 optimal weight: 8.9990 chunk 358 optimal weight: 0.6980 chunk 382 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 361 optimal weight: 0.5980 chunk 381 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN H 43 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34779 Z= 0.215 Angle : 0.534 8.807 47352 Z= 0.270 Chirality : 0.044 0.351 5522 Planarity : 0.004 0.053 6010 Dihedral : 4.651 49.012 5761 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4193 helix: 1.69 (0.22), residues: 644 sheet: -0.21 (0.17), residues: 975 loop : -1.31 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP Q 113 HIS 0.003 0.001 HIS Q 35 PHE 0.022 0.001 PHE C 238 TYR 0.016 0.001 TYR B1067 ARG 0.003 0.000 ARG Q 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9297 (m) cc_final: 0.9022 (p) REVERT: A 962 LEU cc_start: 0.9424 (tp) cc_final: 0.9160 (tt) REVERT: B 786 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7658 (mmtm) REVERT: C 223 LEU cc_start: 0.8037 (mm) cc_final: 0.7822 (mm) REVERT: N 128 LEU cc_start: 0.3689 (mp) cc_final: 0.2606 (tt) REVERT: R 3 GLN cc_start: 0.7217 (tm-30) cc_final: 0.6988 (tm-30) REVERT: R 6 GLN cc_start: 0.7800 (pp30) cc_final: 0.7423 (pp30) REVERT: R 90 ASP cc_start: 0.6840 (m-30) cc_final: 0.6404 (m-30) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3956 time to fit residues: 144.7003 Evaluate side-chains 135 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 424 optimal weight: 8.9990 chunk 390 optimal weight: 4.9990 chunk 337 optimal weight: 0.5980 chunk 35 optimal weight: 0.0270 chunk 261 optimal weight: 0.0870 chunk 207 optimal weight: 3.9990 overall best weight: 1.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN B 955 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN H 43 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34779 Z= 0.226 Angle : 0.538 8.694 47352 Z= 0.272 Chirality : 0.044 0.349 5522 Planarity : 0.004 0.058 6010 Dihedral : 4.646 48.831 5761 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4193 helix: 1.69 (0.21), residues: 641 sheet: -0.20 (0.17), residues: 973 loop : -1.33 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP Q 113 HIS 0.002 0.001 HIS A 954 PHE 0.028 0.001 PHE C 486 TYR 0.021 0.001 TYR B 873 ARG 0.003 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9283 (m) cc_final: 0.9024 (p) REVERT: C 223 LEU cc_start: 0.8124 (mm) cc_final: 0.7921 (mm) REVERT: N 128 LEU cc_start: 0.3720 (mp) cc_final: 0.2622 (tt) REVERT: R 6 GLN cc_start: 0.7915 (pp30) cc_final: 0.7461 (pp30) REVERT: R 90 ASP cc_start: 0.6656 (m-30) cc_final: 0.6353 (m-30) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.4122 time to fit residues: 145.0530 Evaluate side-chains 133 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 0.7980 chunk 360 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 311 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 338 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 347 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 460 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN M 6 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.141654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.114296 restraints weight = 80930.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.114819 restraints weight = 166859.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115554 restraints weight = 133841.631| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34779 Z= 0.200 Angle : 0.525 8.784 47352 Z= 0.265 Chirality : 0.044 0.345 5522 Planarity : 0.004 0.055 6010 Dihedral : 4.598 52.460 5761 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4193 helix: 1.63 (0.21), residues: 651 sheet: -0.16 (0.17), residues: 969 loop : -1.29 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP Q 113 HIS 0.003 0.001 HIS H 35 PHE 0.024 0.001 PHE C 429 TYR 0.016 0.001 TYR B 873 ARG 0.004 0.000 ARG C1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5113.52 seconds wall clock time: 94 minutes 15.92 seconds (5655.92 seconds total)