Starting phenix.real_space_refine on Fri Jul 26 18:32:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbz_39917/07_2024/8zbz_39917.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbz_39917/07_2024/8zbz_39917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbz_39917/07_2024/8zbz_39917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbz_39917/07_2024/8zbz_39917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbz_39917/07_2024/8zbz_39917.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbz_39917/07_2024/8zbz_39917.cif" } resolution = 4.71 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= 0.004 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 21647 2.51 5 N 5562 2.21 5 O 6646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "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 TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 162": "OD1" <-> "OD2" Residue "D TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 90": "OD1" <-> "OD2" Residue "Q GLU 226": "OE1" <-> "OE2" Time to flip residues: 0.54s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 33999 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" 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: "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: "D" 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: "E" 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 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 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.57, per 1000 atoms: 0.49 Number of scatterers: 33999 At special positions: 0 Unit cell: (174.24, 162.36, 241.56, 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 6646 8.00 N 5562 7.00 C 21647 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=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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=2.04 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=2.03 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 D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 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=2.03 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 603 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 122 " " NAG L 1 " - " ASN B 709 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN B 331 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 12.37 Conformation dependent library (CDL) restraints added in 6.1 seconds 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8000 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 76 sheets defined 17.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.328A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 753 removed outlier: 4.070A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.729A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.549A pdb=" N VAL A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 916 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR A 917 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 918 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 918' Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.839A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.594A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.788A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.159A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.279A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.543A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.070A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.633A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.991A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 781 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.507A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.896A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.679A pdb=" N VAL B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 916 " --> pdb=" O GLN B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 916' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.725A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.064A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1147 removed outlier: 3.695A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.841A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.689A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.638A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 753 removed outlier: 3.656A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 757 Processing helix chain 'C' and resid 758 through 781 removed outlier: 4.220A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (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 910 removed outlier: 3.541A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.511A pdb=" N VAL C 915 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR C 917 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 918 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.525A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 989 through 1033 Processing helix chain 'D' and resid 132 through 137 removed outlier: 3.800A pdb=" N LEU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.751A pdb=" N HIS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 removed outlier: 3.771A pdb=" N ARG E 110 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET E 112 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 172 No H-bonds generated for 'chain 'E' and resid 170 through 172' Processing helix chain 'E' and resid 199 through 204 removed outlier: 3.699A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 204' Processing helix chain 'M' and resid 134 through 139 removed outlier: 3.716A pdb=" N GLN M 137 " --> pdb=" O GLU M 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN M 139 " --> pdb=" O LEU M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 197 removed outlier: 3.508A pdb=" N LYS M 197 " --> pdb=" O PRO M 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 137 removed outlier: 3.608A pdb=" N LEU N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 198 Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.796A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 172 No H-bonds generated for 'chain 'Q' and resid 170 through 172' Processing helix chain 'R' and resid 105 through 109 removed outlier: 3.747A pdb=" N GLN R 109 " --> pdb=" O ASN R 106 " (cutoff:3.500A) 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 30 removed outlier: 8.400A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.568A pdb=" N PHE A 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.528A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.706A 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: 3.851A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.912A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.843A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.598A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.845A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.845A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 392 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.685A pdb=" N TYR A 453 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.953A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 719 removed outlier: 7.147A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 728 removed outlier: 3.736A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 3.760A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.578A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.573A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 55 removed outlier: 4.050A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.916A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.191A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.031A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 357 removed outlier: 3.530A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.447A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 713 through 728 removed outlier: 6.942A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD1, first strand: chain 'B' and resid 1076 through 1077 removed outlier: 3.640A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 3.615A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.053A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.850A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.641A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.835A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 207 through 209 removed outlier: 4.071A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 207 through 209 removed outlier: 3.729A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 313 through 317 removed outlier: 6.885A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.806A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.489A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 399 through 402 removed outlier: 3.543A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) 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 539 through 543 removed outlier: 3.693A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 655 through 656 removed outlier: 4.295A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.515A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 719 removed outlier: 3.759A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 719 removed outlier: 3.759A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.656A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.733A pdb=" N ALA D 72 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE D 64 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 46 through 50 removed outlier: 3.776A pdb=" N LEU D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP D 93 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.795A pdb=" N SER D 148 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 171 " --> pdb=" O TYR D 188 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 206 through 207 removed outlier: 4.709A pdb=" N VAL D 206 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 213 " --> pdb=" O VAL D 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.887A pdb=" N VAL E 5 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 23 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 81 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.897A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL E 37 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN E 39 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS E 96 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY E 118 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 150 through 153 Processing sheet with id=AG1, first strand: chain 'E' and resid 156 through 157 removed outlier: 4.035A pdb=" N VAL E 156 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 192 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER E 191 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL E 183 " --> pdb=" O SER E 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'E' and resid 166 through 168 removed outlier: 3.866A pdb=" N SER E 167 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN E 211 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS E 210 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS E 223 " --> pdb=" O CYS E 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'M' and resid 9 through 12 removed outlier: 4.289A pdb=" N THR M 108 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 9 through 12 removed outlier: 4.289A pdb=" N THR M 108 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 18 through 23 removed outlier: 3.622A pdb=" N PHE M 64 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 128 through 129 removed outlier: 3.541A pdb=" N PHE M 129 " --> pdb=" O VAL M 144 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL M 144 " --> pdb=" O PHE M 129 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS M 145 " --> pdb=" O SER M 187 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR M 183 " --> pdb=" O ASP M 149 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 141 through 142 Processing sheet with id=AG8, first strand: chain 'M' and resid 157 through 160 removed outlier: 3.900A pdb=" N LYS M 160 " --> pdb=" O SER M 203 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER M 203 " --> pdb=" O LYS M 160 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS M 204 " --> pdb=" O LYS M 215 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS M 215 " --> pdb=" O CYS M 204 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL M 206 " --> pdb=" O VAL M 213 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL M 213 " --> pdb=" O VAL M 206 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.836A pdb=" N ILE N 76 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE N 20 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 45 through 50 removed outlier: 7.019A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN N 39 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP N 93 " --> pdb=" O GLY N 98 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY N 98 " --> pdb=" O ASP N 93 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 45 through 50 removed outlier: 7.019A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN N 39 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR N 105 " --> pdb=" O TYR N 87 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 125 through 129 removed outlier: 3.787A pdb=" N PHE N 129 " --> pdb=" O VAL N 144 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL N 144 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA N 184 " --> pdb=" O SER N 176 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AH5, first strand: chain 'N' and resid 171 through 172 Processing sheet with id=AH6, first strand: chain 'Q' and resid 46 through 47 removed outlier: 3.616A pdb=" N VAL Q 37 " --> pdb=" O PHE Q 95 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR Q 116 " --> pdb=" O ARG Q 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 46 through 47 removed outlier: 3.616A pdb=" N VAL Q 37 " --> pdb=" O PHE Q 95 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA Q 92 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL Q 123 " --> pdb=" O ALA Q 92 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR Q 94 " --> pdb=" O ALA Q 121 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA Q 121 " --> pdb=" O TYR Q 94 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 68 through 70 removed outlier: 3.503A pdb=" N THR Q 69 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU Q 82 " --> pdb=" O THR Q 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'Q' and resid 165 through 168 removed outlier: 4.076A pdb=" N THR Q 165 " --> pdb=" O ASN Q 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL Q 212 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL Q 221 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS Q 214 " --> pdb=" O THR Q 219 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR Q 219 " --> pdb=" O HIS Q 214 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'R' and resid 58 through 60 removed outlier: 3.822A pdb=" N ASN R 59 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL R 93 " --> pdb=" O GLN R 39 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR R 116 " --> pdb=" O ARG R 98 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 71 through 72 removed outlier: 4.385A pdb=" N THR R 71 " --> pdb=" O TYR R 80 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR R 80 " --> pdb=" O THR R 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'R' and resid 135 through 137 removed outlier: 4.361A pdb=" N LEU R 152 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL R 196 " --> pdb=" O LEU R 152 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 165 through 168 932 hydrogen bonds defined for protein. 2547 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: 14.53 Time building geometry restraints manager: 13.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10684 1.34 - 1.47: 8724 1.47 - 1.59: 15215 1.59 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 34803 Sorted by residual: bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.38e-02 5.25e+03 1.15e+01 bond pdb=" CG PRO Q 163 " pdb=" CD PRO Q 163 " ideal model delta sigma weight residual 1.512 1.446 0.066 2.70e-02 1.37e+03 5.96e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.88e+00 ... (remaining 34798 not shown) Histogram of bond angle deviations from ideal: 96.74 - 104.27: 603 104.27 - 111.79: 16451 111.79 - 119.32: 11973 119.32 - 126.85: 17906 126.85 - 134.37: 453 Bond angle restraints: 47386 Sorted by residual: angle pdb=" N PRO Q 163 " pdb=" CD PRO Q 163 " pdb=" CG PRO Q 163 " ideal model delta sigma weight residual 103.80 97.92 5.88 1.20e+00 6.94e-01 2.40e+01 angle pdb=" N THR A 470 " pdb=" CA THR A 470 " pdb=" C THR A 470 " ideal model delta sigma weight residual 114.56 109.52 5.04 1.27e+00 6.20e-01 1.57e+01 angle pdb=" CA PRO Q 163 " pdb=" N PRO Q 163 " pdb=" CD PRO Q 163 " ideal model delta sigma weight residual 111.50 105.97 5.53 1.40e+00 5.10e-01 1.56e+01 angle pdb=" CB PRO Q 163 " pdb=" CG PRO Q 163 " pdb=" CD PRO Q 163 " ideal model delta sigma weight residual 105.40 96.74 8.66 2.30e+00 1.89e-01 1.42e+01 angle pdb=" C GLU Q 162 " pdb=" N PRO Q 163 " pdb=" CD PRO Q 163 " ideal model delta sigma weight residual 120.60 112.42 8.18 2.20e+00 2.07e-01 1.38e+01 ... (remaining 47381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 20005 21.80 - 43.60: 1272 43.60 - 65.40: 146 65.40 - 87.21: 76 87.21 - 109.01: 13 Dihedral angle restraints: 21512 sinusoidal: 9083 harmonic: 12429 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.77 83.23 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 12.77 80.23 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -8.43 -77.57 1 1.00e+01 1.00e-02 7.53e+01 ... (remaining 21509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 5490 0.130 - 0.260: 38 0.260 - 0.390: 5 0.390 - 0.521: 1 0.521 - 0.651: 2 Chirality restraints: 5536 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.61e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 5533 not shown) Planarity restraints: 6050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " 0.336 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG C1304 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.327 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG B1305 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.501 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 162 " -0.069 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO Q 163 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO Q 163 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO Q 163 " -0.045 5.00e-02 4.00e+02 ... (remaining 6047 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 192 2.54 - 3.13: 23570 3.13 - 3.72: 50526 3.72 - 4.31: 66147 4.31 - 4.90: 110919 Nonbonded interactions: 251354 Sorted by model distance: nonbonded pdb=" OG SER Q 126 " pdb=" CZ PHE Q 160 " model vdw 1.945 3.340 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.222 2.440 nonbonded pdb=" OG SER Q 126 " pdb=" CE1 PHE Q 160 " model vdw 2.252 3.340 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.257 2.440 nonbonded pdb=" OG SER A1030 " pdb=" OD2 ASP B1041 " model vdw 2.259 2.440 ... (remaining 251349 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 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1147 or resid 1301 through 1305)) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1147 or resid 1301 through 1305)) 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 1305)) } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' 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 'Z' } ncs_group { reference = chain 'I' selection = chain 'Y' } 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.300 Process input model: 84.060 Find NCS groups from input model: 4.780 Set up NCS constraints: 0.270 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34803 Z= 0.231 Angle : 0.688 10.054 47386 Z= 0.351 Chirality : 0.050 0.651 5536 Planarity : 0.008 0.292 6009 Dihedral : 14.174 109.008 13359 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % 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: -1.66 (0.12), residues: 4192 helix: -0.17 (0.19), residues: 645 sheet: 0.07 (0.20), residues: 701 loop : -1.75 (0.11), residues: 2846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 196 HIS 0.006 0.001 HIS E 35 PHE 0.042 0.001 PHE C 55 TYR 0.025 0.001 TYR D 37 ARG 0.012 0.000 ARG R 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 3.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7775 (mm) cc_final: 0.7413 (mm) REVERT: A 985 ASP cc_start: 0.9151 (m-30) cc_final: 0.8797 (t0) REVERT: B 238 PHE cc_start: 0.8320 (t80) cc_final: 0.8023 (t80) REVERT: B 497 PHE cc_start: 0.4958 (m-10) cc_final: 0.4532 (m-10) REVERT: B 498 ARG cc_start: 0.6442 (mmt-90) cc_final: 0.4810 (mmp80) REVERT: B 562 PHE cc_start: 0.7341 (p90) cc_final: 0.7092 (p90) REVERT: B 712 ILE cc_start: 0.8725 (tt) cc_final: 0.8467 (tt) REVERT: B 868 GLU cc_start: 0.8145 (pm20) cc_final: 0.7881 (mp0) REVERT: C 141 LEU cc_start: 0.8375 (mm) cc_final: 0.8031 (tp) REVERT: C 1018 ILE cc_start: 0.8841 (tp) cc_final: 0.8487 (tp) REVERT: C 1041 ASP cc_start: 0.7391 (t0) cc_final: 0.6889 (t0) REVERT: D 150 PHE cc_start: 0.6463 (p90) cc_final: 0.5813 (p90) REVERT: E 73 ASP cc_start: 0.6237 (t0) cc_final: 0.5985 (t0) REVERT: E 215 LYS cc_start: 0.7390 (pttp) cc_final: 0.6408 (tttp) outliers start: 4 outliers final: 1 residues processed: 211 average time/residue: 0.4109 time to fit residues: 149.8208 Evaluate side-chains 134 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 3.324 ------------------------------------------------------------------------------- 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: 7.9990 chunk 322 optimal weight: 0.4980 chunk 179 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 333 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 386 optimal weight: 30.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 777 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN D 195 GLN E 43 GLN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN R 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34803 Z= 0.184 Angle : 0.532 11.250 47386 Z= 0.269 Chirality : 0.044 0.458 5536 Planarity : 0.004 0.076 6009 Dihedral : 6.541 59.939 5818 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % 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: -1.15 (0.13), residues: 4192 helix: 0.90 (0.21), residues: 651 sheet: -0.07 (0.18), residues: 808 loop : -1.48 (0.11), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.010 0.001 HIS A 954 PHE 0.013 0.001 PHE C 377 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8248 (mm) cc_final: 0.7948 (mm) REVERT: A 429 PHE cc_start: 0.7238 (t80) cc_final: 0.7013 (t80) REVERT: A 881 THR cc_start: 0.8322 (m) cc_final: 0.8119 (p) REVERT: B 238 PHE cc_start: 0.8292 (t80) cc_final: 0.7948 (t80) REVERT: B 562 PHE cc_start: 0.7588 (p90) cc_final: 0.7305 (p90) REVERT: B 712 ILE cc_start: 0.9103 (tt) cc_final: 0.8748 (tt) REVERT: C 55 PHE cc_start: 0.7576 (m-10) cc_final: 0.7371 (m-10) REVERT: C 390 LEU cc_start: 0.8668 (mm) cc_final: 0.8390 (tp) REVERT: C 1018 ILE cc_start: 0.8879 (tp) cc_final: 0.8608 (tp) REVERT: C 1041 ASP cc_start: 0.7312 (t0) cc_final: 0.6988 (t70) REVERT: D 52 ASN cc_start: 0.5043 (t160) cc_final: 0.4833 (m-40) REVERT: Q 112 MET cc_start: 0.7716 (mtt) cc_final: 0.7499 (mtt) REVERT: R 70 MET cc_start: 0.5847 (mmm) cc_final: 0.4826 (mmm) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.4220 time to fit residues: 135.0702 Evaluate side-chains 127 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 3.631 ------------------------------------------------------------------------------- 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: 5.9990 chunk 120 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 263 optimal weight: 0.4980 chunk 106 optimal weight: 0.0020 chunk 387 optimal weight: 20.0000 chunk 418 optimal weight: 0.4980 chunk 345 optimal weight: 4.9990 chunk 384 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 310 optimal weight: 20.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** E 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN Q 6 GLN R 33 ASN R 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34803 Z= 0.170 Angle : 0.505 12.015 47386 Z= 0.255 Chirality : 0.044 0.417 5536 Planarity : 0.004 0.076 6009 Dihedral : 5.752 58.339 5818 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.45 % 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: -0.97 (0.13), residues: 4192 helix: 1.19 (0.21), residues: 650 sheet: -0.01 (0.18), residues: 840 loop : -1.40 (0.12), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.008 0.001 HIS A 954 PHE 0.027 0.001 PHE B 898 TYR 0.014 0.001 TYR D 50 ARG 0.007 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 3.802 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7200 (t80) cc_final: 0.6920 (t80) REVERT: B 238 PHE cc_start: 0.8387 (t80) cc_final: 0.8004 (t80) REVERT: B 562 PHE cc_start: 0.7606 (p90) cc_final: 0.7249 (p90) REVERT: B 712 ILE cc_start: 0.9197 (tt) cc_final: 0.8869 (tt) REVERT: C 55 PHE cc_start: 0.7797 (m-10) cc_final: 0.7540 (m-10) REVERT: C 1018 ILE cc_start: 0.8932 (tp) cc_final: 0.8672 (tp) REVERT: C 1041 ASP cc_start: 0.7301 (t0) cc_final: 0.6951 (t0) REVERT: R 98 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7814 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.4233 time to fit residues: 128.8135 Evaluate side-chains 118 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 4.079 ------------------------------------------------------------------------------- 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: 20.0000 chunk 291 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 chunk 260 optimal weight: 0.9980 chunk 388 optimal weight: 10.0000 chunk 411 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 overall best weight: 3.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 777 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 66 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 901 GLN B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN Q 6 GLN R 43 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34803 Z= 0.255 Angle : 0.584 9.748 47386 Z= 0.298 Chirality : 0.045 0.422 5536 Planarity : 0.005 0.074 6009 Dihedral : 5.753 57.297 5818 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % 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: -1.06 (0.13), residues: 4192 helix: 1.04 (0.21), residues: 645 sheet: -0.20 (0.18), residues: 850 loop : -1.38 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP M 196 HIS 0.007 0.001 HIS A1048 PHE 0.028 0.002 PHE C 275 TYR 0.051 0.001 TYR D 50 ARG 0.011 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7742 (m-80) cc_final: 0.7474 (m-80) REVERT: B 562 PHE cc_start: 0.7668 (p90) cc_final: 0.7310 (p90) REVERT: C 1041 ASP cc_start: 0.7336 (t0) cc_final: 0.6951 (t0) REVERT: D 50 TYR cc_start: 0.3257 (p90) cc_final: 0.2796 (p90) REVERT: R 159 TYR cc_start: 0.6000 (p90) cc_final: 0.5757 (p90) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.4219 time to fit residues: 113.0936 Evaluate side-chains 110 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 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: 6.9990 chunk 233 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 306 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 369 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 804 GLN B 935 GLN B 955 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN R 178 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 34803 Z= 0.346 Angle : 0.688 10.247 47386 Z= 0.352 Chirality : 0.048 0.438 5536 Planarity : 0.005 0.071 6009 Dihedral : 6.514 58.506 5818 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % 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: -1.53 (0.13), residues: 4192 helix: 0.46 (0.20), residues: 646 sheet: -0.56 (0.17), residues: 864 loop : -1.63 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 886 HIS 0.008 0.002 HIS A1083 PHE 0.028 0.002 PHE C 275 TYR 0.022 0.002 TYR C 873 ARG 0.010 0.001 ARG Q 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7594 (m-80) cc_final: 0.7269 (m-80) REVERT: B 238 PHE cc_start: 0.8669 (t80) cc_final: 0.8109 (t80) REVERT: C 1041 ASP cc_start: 0.7521 (t0) cc_final: 0.7156 (t70) REVERT: D 50 TYR cc_start: 0.3246 (p90) cc_final: 0.2642 (p90) REVERT: D 64 PHE cc_start: 0.6195 (t80) cc_final: 0.5920 (t80) REVERT: R 70 MET cc_start: 0.7406 (mmm) cc_final: 0.7184 (mmp) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.4188 time to fit residues: 107.9007 Evaluate side-chains 108 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 3.653 ------------------------------------------------------------------------------- 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: 30.0000 chunk 370 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 412 optimal weight: 10.0000 chunk 342 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 136 optimal weight: 0.1980 chunk 216 optimal weight: 6.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN B 955 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34803 Z= 0.293 Angle : 0.629 9.701 47386 Z= 0.322 Chirality : 0.047 0.433 5536 Planarity : 0.005 0.073 6009 Dihedral : 6.268 56.587 5818 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 4192 helix: 0.56 (0.20), residues: 646 sheet: -0.53 (0.17), residues: 903 loop : -1.65 (0.12), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 196 HIS 0.008 0.001 HIS A1048 PHE 0.035 0.002 PHE C 275 TYR 0.025 0.002 TYR A 660 ARG 0.012 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7543 (m-80) cc_final: 0.7220 (m-80) REVERT: B 902 MET cc_start: 0.8375 (tpp) cc_final: 0.7989 (tpp) REVERT: C 1041 ASP cc_start: 0.7607 (t0) cc_final: 0.7260 (t70) REVERT: D 64 PHE cc_start: 0.6250 (t80) cc_final: 0.5970 (t80) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.4303 time to fit residues: 108.9158 Evaluate side-chains 102 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 3.968 ------------------------------------------------------------------------------- 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: 40.0000 chunk 46 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 346 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 410 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 613 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 HIS R 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34803 Z= 0.347 Angle : 0.686 11.332 47386 Z= 0.350 Chirality : 0.048 0.448 5536 Planarity : 0.005 0.065 6009 Dihedral : 6.628 58.333 5818 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.13), residues: 4192 helix: 0.32 (0.20), residues: 650 sheet: -0.67 (0.17), residues: 892 loop : -1.80 (0.12), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 50 HIS 0.009 0.002 HIS A1048 PHE 0.027 0.002 PHE C 275 TYR 0.039 0.002 TYR C 796 ARG 0.006 0.001 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7495 (m-80) cc_final: 0.7265 (m-80) REVERT: A 731 MET cc_start: 0.8973 (pmm) cc_final: 0.8744 (pmm) REVERT: B 902 MET cc_start: 0.8528 (tpp) cc_final: 0.8211 (tpp) REVERT: C 697 MET cc_start: 0.7947 (ttm) cc_final: 0.7678 (ttt) REVERT: D 64 PHE cc_start: 0.6484 (t80) cc_final: 0.6214 (t80) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.4379 time to fit residues: 105.9204 Evaluate side-chains 100 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 3.622 ------------------------------------------------------------------------------- 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: 1.9990 chunk 163 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 322 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 955 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34803 Z= 0.163 Angle : 0.562 9.649 47386 Z= 0.284 Chirality : 0.046 0.401 5536 Planarity : 0.004 0.063 6009 Dihedral : 5.847 56.587 5818 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -1.32 (0.13), residues: 4192 helix: 0.96 (0.21), residues: 640 sheet: -0.42 (0.17), residues: 899 loop : -1.58 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 50 HIS 0.010 0.001 HIS A 954 PHE 0.024 0.001 PHE C 55 TYR 0.022 0.001 TYR D 50 ARG 0.006 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7548 (m-80) cc_final: 0.7300 (m-80) REVERT: A 731 MET cc_start: 0.8918 (pmm) cc_final: 0.8678 (pmm) REVERT: B 902 MET cc_start: 0.8370 (tpp) cc_final: 0.8041 (tpp) REVERT: N 101 PHE cc_start: 0.8454 (m-10) cc_final: 0.7630 (p90) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.4349 time to fit residues: 112.8202 Evaluate side-chains 108 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 3.633 ------------------------------------------------------------------------------- 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: 10.0000 chunk 393 optimal weight: 5.9990 chunk 358 optimal weight: 4.9990 chunk 382 optimal weight: 30.0000 chunk 230 optimal weight: 0.0370 chunk 166 optimal weight: 7.9990 chunk 300 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 345 optimal weight: 10.0000 chunk 361 optimal weight: 2.9990 chunk 381 optimal weight: 30.0000 overall best weight: 3.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34803 Z= 0.237 Angle : 0.586 9.681 47386 Z= 0.296 Chirality : 0.046 0.408 5536 Planarity : 0.004 0.064 6009 Dihedral : 5.852 56.990 5818 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.03 % Allowed : 0.54 % Favored : 99.43 % 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: -1.37 (0.13), residues: 4192 helix: 0.93 (0.21), residues: 643 sheet: -0.54 (0.17), residues: 890 loop : -1.58 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 50 HIS 0.009 0.001 HIS A 954 PHE 0.022 0.001 PHE C 275 TYR 0.027 0.001 TYR D 50 ARG 0.009 0.000 ARG Q 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 3.690 Fit side-chains revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7558 (m-80) cc_final: 0.7318 (m-80) REVERT: A 731 MET cc_start: 0.8961 (pmm) cc_final: 0.8738 (pmm) REVERT: B 238 PHE cc_start: 0.8644 (t80) cc_final: 0.8140 (t80) REVERT: B 902 MET cc_start: 0.8404 (tpp) cc_final: 0.8029 (tpp) REVERT: N 101 PHE cc_start: 0.8182 (m-10) cc_final: 0.7655 (p90) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.4275 time to fit residues: 100.7222 Evaluate side-chains 100 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 3.778 ------------------------------------------------------------------------------- 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: 10.0000 chunk 404 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 281 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 chunk 390 optimal weight: 30.0000 chunk 337 optimal weight: 0.0970 chunk 35 optimal weight: 6.9990 chunk 261 optimal weight: 0.3980 chunk 207 optimal weight: 6.9990 overall best weight: 3.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 52 ASN E 211 ASN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34803 Z= 0.267 Angle : 0.614 10.312 47386 Z= 0.312 Chirality : 0.046 0.415 5536 Planarity : 0.004 0.065 6009 Dihedral : 6.031 56.785 5818 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.03 % Allowed : 0.62 % Favored : 99.35 % 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 (0.13), residues: 4192 helix: 0.79 (0.21), residues: 646 sheet: -0.61 (0.17), residues: 906 loop : -1.66 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Q 113 HIS 0.008 0.001 HIS A 954 PHE 0.033 0.002 PHE C 55 TYR 0.026 0.002 TYR D 50 ARG 0.013 0.001 ARG D 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8949 (pmm) cc_final: 0.8724 (pmm) REVERT: B 238 PHE cc_start: 0.8647 (t80) cc_final: 0.8144 (t80) REVERT: B 902 MET cc_start: 0.8541 (tpp) cc_final: 0.8166 (tpp) REVERT: N 101 PHE cc_start: 0.8163 (m-10) cc_final: 0.7628 (p90) REVERT: Q 112 MET cc_start: 0.8245 (mtt) cc_final: 0.7898 (mtt) REVERT: R 98 ARG cc_start: 0.8782 (ttp80) cc_final: 0.8577 (ttp80) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.4207 time to fit residues: 98.2305 Evaluate side-chains 95 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 3.908 ------------------------------------------------------------------------------- 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: 0.2980 chunk 360 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 311 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 93 optimal weight: 0.2980 chunk 338 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 347 optimal weight: 0.0980 chunk 42 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN R 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.081907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062529 restraints weight = 214223.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061279 restraints weight = 166257.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.061839 restraints weight = 166676.775| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34803 Z= 0.140 Angle : 0.541 9.747 47386 Z= 0.270 Chirality : 0.045 0.396 5536 Planarity : 0.004 0.065 6009 Dihedral : 5.337 56.509 5818 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -1.14 (0.13), residues: 4192 helix: 1.17 (0.21), residues: 641 sheet: -0.40 (0.18), residues: 879 loop : -1.44 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 50 HIS 0.006 0.001 HIS A1048 PHE 0.025 0.001 PHE A 201 TYR 0.020 0.001 TYR D 50 ARG 0.006 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4648.06 seconds wall clock time: 86 minutes 32.47 seconds (5192.47 seconds total)