Starting phenix.real_space_refine on Thu Feb 22 05:52:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0x_26267/02_2024/7u0x_26267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0x_26267/02_2024/7u0x_26267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0x_26267/02_2024/7u0x_26267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0x_26267/02_2024/7u0x_26267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0x_26267/02_2024/7u0x_26267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0x_26267/02_2024/7u0x_26267.pdb" } resolution = 3.82 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= -0.003 sd= 0.058 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 20954 2.51 5 N 5461 2.21 5 O 6515 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 TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "F ASP 57": "OD1" <-> "OD2" Residue "F TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 61": "OD1" <-> "OD2" Residue "G ASP 88": "OD1" <-> "OD2" Residue "G TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 52": "OD1" <-> "OD2" Residue "L ASP 68": "OD1" <-> "OD2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33074 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8494 Classifications: {'peptide': 1085} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 4 Chain: "B" Number of atoms: 8515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "C" Number of atoms: 8502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8502 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 59, 'TRANS': 1027} Chain breaks: 4 Chain: "F" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1738 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1627 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "H" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1745 Classifications: {'peptide': 234} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Chain: "L" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1627 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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: "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: 17.97, per 1000 atoms: 0.54 Number of scatterers: 33074 At special positions: 0 Unit cell: (163.572, 165.711, 210.613, 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 6515 8.00 N 5461 7.00 C 20954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 110 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 212 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 110 " distance=2.02 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 212 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 343 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 343 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 17 " " NAG C1311 " - " ASN C 343 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A1134 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 709 " " NAG M 1 " - " ASN A 17 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " Time building additional restraints: 13.82 Conformation dependent library (CDL) restraints added in 5.6 seconds 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7754 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 79 sheets defined 20.8% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.589A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.535A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.673A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.115A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.558A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.928A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.625A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 890 removed outlier: 3.987A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.606A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.821A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.904A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.550A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.934A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.582A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.774A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.409A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.528A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.739A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.650A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 632 through 638 Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.575A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.676A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.506A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 removed outlier: 4.113A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.563A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.968A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.161A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.726A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.352A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1149 removed outlier: 4.541A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.555A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 632 through 638 removed outlier: 3.816A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 756 No H-bonds generated for 'chain 'C' and resid 755 through 756' Processing helix chain 'C' and resid 757 through 760 removed outlier: 3.722A pdb=" N CYS C 760 " --> pdb=" O GLY C 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 757 through 760' Processing helix chain 'C' and resid 761 through 782 removed outlier: 3.887A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (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 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.573A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.901A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.530A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.513A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.341A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.909A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 127 through 132 removed outlier: 3.609A pdb=" N GLN G 130 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 192 removed outlier: 3.504A pdb=" N HIS G 192 " --> pdb=" O GLN G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 removed outlier: 3.731A pdb=" N GLU G 214 " --> pdb=" O ALA G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.889A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 removed outlier: 4.251A pdb=" N GLN L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 192 removed outlier: 3.775A pdb=" N SER L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS L 192 " --> pdb=" O GLN L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.241A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N TRP A 64 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL A 267 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N HIS A 66 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR A 265 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 5.538A pdb=" N TRP A 64 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL A 267 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N HIS A 66 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR A 265 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.516A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.088A 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: 3.684A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 155 removed outlier: 3.581A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.591A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.591A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.564A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 359 removed outlier: 4.509A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.030A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.122A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.294A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A1065 " --> pdb=" O MET A1050 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.294A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.800A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.611A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.595A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.023A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 151 through 155 removed outlier: 3.807A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.490A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.935A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.806A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.575A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.693A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.276A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.276A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.607A pdb=" N HIS B1083 " --> pdb=" O LYS B1086 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.733A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.733A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.727A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.088A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 151 through 155 removed outlier: 3.783A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.714A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.445A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.484A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.709A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.097A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 714 Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.872A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.250A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.601A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.854A pdb=" N SER F 7 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 58 through 59 removed outlier: 6.968A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL F 37 " --> pdb=" O TYR F 95 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.889A pdb=" N SER F 136 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS F 159 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU F 154 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL F 198 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS F 156 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER F 196 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL F 158 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR F 192 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL F 197 " --> pdb=" O HIS F 180 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.889A pdb=" N SER F 136 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS F 159 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU F 154 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL F 198 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS F 156 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER F 196 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL F 158 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR F 192 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 166 through 167 Processing sheet with id=AG5, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.741A pdb=" N THR G 23 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AG7, first strand: chain 'G' and resid 33 through 34 removed outlier: 4.096A pdb=" N TYR G 33 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR G 94 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER G 93 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL G 100 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AG9, first strand: chain 'G' and resid 118 through 122 removed outlier: 4.194A pdb=" N SER G 118 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER G 141 " --> pdb=" O SER G 118 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 120 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 139 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL G 137 " --> pdb=" O PHE G 122 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA G 134 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR G 176 " --> pdb=" O ASP G 142 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR G 181 " --> pdb=" O GLU G 164 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU G 164 " --> pdb=" O TYR G 181 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 118 through 122 removed outlier: 4.194A pdb=" N SER G 118 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER G 141 " --> pdb=" O SER G 118 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 120 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 139 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL G 137 " --> pdb=" O PHE G 122 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA G 134 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR G 176 " --> pdb=" O ASP G 142 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 157 through 159 removed outlier: 4.483A pdb=" N TRP G 152 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.194A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.194A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AH6, first strand: chain 'H' and resid 34 through 37 Processing sheet with id=AH7, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.523A pdb=" N TYR H 59 " --> pdb=" O PHE H 50 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 139 through 140 removed outlier: 3.530A pdb=" N LEU H 140 " --> pdb=" O GLY H 155 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY H 155 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL H 200 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU H 154 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL H 198 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER H 196 " --> pdb=" O CYS H 156 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 158 through 161 removed outlier: 3.661A pdb=" N VAL H 158 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 167 through 170 Processing sheet with id=AI2, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.193A pdb=" N THR L 23 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU L 76 " --> pdb=" O ILE L 20 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.197A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR L 89 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN L 38 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N THR L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.197A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR L 89 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS L 92 " --> pdb=" O GLN L 35 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER L 93 " --> pdb=" O VAL L 100 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 119 through 122 removed outlier: 4.084A pdb=" N THR L 120 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU L 139 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 119 through 122 removed outlier: 4.084A pdb=" N THR L 120 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU L 139 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.188A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA L 151 " --> pdb=" O GLN L 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN L 198 " --> pdb=" O ALA L 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS L 153 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER L 196 " --> pdb=" O LYS L 153 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3036 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: 17.30 Time building geometry restraints manager: 14.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5357 1.28 - 1.41: 8467 1.41 - 1.55: 19797 1.55 - 1.68: 43 1.68 - 1.82: 180 Bond restraints: 33844 Sorted by residual: bond pdb=" C GLU L 51 " pdb=" O GLU L 51 " ideal model delta sigma weight residual 1.235 1.141 0.095 1.26e-02 6.30e+03 5.64e+01 bond pdb=" N GLU L 51 " pdb=" CA GLU L 51 " ideal model delta sigma weight residual 1.457 1.367 0.091 1.29e-02 6.01e+03 4.92e+01 bond pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " ideal model delta sigma weight residual 1.527 1.592 -0.066 1.75e-02 3.27e+03 1.40e+01 bond pdb=" N ASP A 427 " pdb=" CA ASP A 427 " ideal model delta sigma weight residual 1.459 1.415 0.043 1.16e-02 7.43e+03 1.39e+01 bond pdb=" C PRO L 7 " pdb=" N HIS L 8 " ideal model delta sigma weight residual 1.334 1.295 0.039 1.43e-02 4.89e+03 7.45e+00 ... (remaining 33839 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.07: 844 106.07 - 113.07: 18516 113.07 - 120.08: 11079 120.08 - 127.09: 15301 127.09 - 134.09: 351 Bond angle restraints: 46091 Sorted by residual: angle pdb=" O TYR L 50 " pdb=" C TYR L 50 " pdb=" N GLU L 51 " ideal model delta sigma weight residual 123.44 130.92 -7.48 1.23e+00 6.61e-01 3.70e+01 angle pdb=" C GLU L 51 " pdb=" N ASP L 52 " pdb=" CA ASP L 52 " ideal model delta sigma weight residual 121.54 132.83 -11.29 1.91e+00 2.74e-01 3.49e+01 angle pdb=" N ASP A 427 " pdb=" CA ASP A 427 " pdb=" C ASP A 427 " ideal model delta sigma weight residual 111.02 103.91 7.11 1.22e+00 6.72e-01 3.40e+01 angle pdb=" CA TYR L 50 " pdb=" C TYR L 50 " pdb=" N GLU L 51 " ideal model delta sigma weight residual 116.29 108.41 7.88 1.45e+00 4.76e-01 2.95e+01 angle pdb=" CA PRO L 7 " pdb=" C PRO L 7 " pdb=" O PRO L 7 " ideal model delta sigma weight residual 120.60 129.57 -8.97 1.82e+00 3.02e-01 2.43e+01 ... (remaining 46086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18268 17.96 - 35.92: 1961 35.92 - 53.88: 495 53.88 - 71.84: 97 71.84 - 89.80: 38 Dihedral angle restraints: 20859 sinusoidal: 8777 harmonic: 12082 Sorted by residual: dihedral pdb=" CB CYS H 105 " pdb=" SG CYS H 105 " pdb=" SG CYS H 110 " pdb=" CB CYS H 110 " ideal model delta sinusoidal sigma weight residual 93.00 20.35 72.65 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 33.41 59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 148.02 -55.02 1 1.00e+01 1.00e-02 4.10e+01 ... (remaining 20856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4538 0.060 - 0.120: 782 0.120 - 0.180: 45 0.180 - 0.239: 7 0.239 - 0.299: 1 Chirality restraints: 5373 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 5370 not shown) Planarity restraints: 5938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 51 " 0.034 2.00e-02 2.50e+03 7.14e-02 5.09e+01 pdb=" C GLU L 51 " -0.123 2.00e-02 2.50e+03 pdb=" O GLU L 51 " 0.048 2.00e-02 2.50e+03 pdb=" N ASP L 52 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 56 " 0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO C 57 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 55 " -0.054 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO L 56 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO L 56 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 56 " -0.045 5.00e-02 4.00e+02 ... (remaining 5935 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 59 2.35 - 2.99: 17150 2.99 - 3.62: 47286 3.62 - 4.26: 69515 4.26 - 4.90: 116909 Nonbonded interactions: 250919 Sorted by model distance: nonbonded pdb=" CB ARG A 408 " pdb=" NE2 GLN L 54 " model vdw 1.712 3.520 nonbonded pdb=" OG SER H 219 " pdb=" OG1 THR H 221 " model vdw 2.198 2.440 nonbonded pdb=" O ILE C 569 " pdb=" OG1 THR C 572 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OG1 THR B 998 " model vdw 2.203 2.440 nonbonded pdb=" O THR B 747 " pdb=" OG SER B 750 " model vdw 2.204 2.440 ... (remaining 250914 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 14 through 178 or resid 185 through 1149 or resid 1301 thr \ ough 1308)) selection = (chain 'B' and (resid 14 through 178 or resid 185 through 623 or resid 633 throu \ gh 1149 or resid 1301 through 1308)) selection = (chain 'C' and (resid 14 through 70 or resid 76 through 623 or resid 633 through \ 1149 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'F' selection = (chain 'H' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 234)) } ncs_group { reference = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 19.020 Check model and map are aligned: 0.440 Set scattering table: 0.340 Process input model: 90.350 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5623 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 0.095 33844 Z= 0.215 Angle : 0.587 11.286 46091 Z= 0.301 Chirality : 0.045 0.299 5373 Planarity : 0.004 0.092 5894 Dihedral : 15.884 89.795 13048 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 0.39 % Allowed : 23.07 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.35 (0.13), residues: 4122 helix: 1.63 (0.21), residues: 672 sheet: -0.26 (0.17), residues: 998 loop : -0.74 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 886 HIS 0.009 0.001 HIS H 216 PHE 0.020 0.001 PHE H 29 TYR 0.024 0.001 TYR C 904 ARG 0.005 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 409 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7752 (mttt) cc_final: 0.7443 (ttmp) REVERT: A 544 ASN cc_start: 0.7782 (t0) cc_final: 0.7015 (p0) REVERT: A 950 ASP cc_start: 0.8389 (t0) cc_final: 0.8053 (t0) REVERT: A 978 ASN cc_start: 0.7028 (m-40) cc_final: 0.6740 (t0) REVERT: A 990 GLU cc_start: 0.7311 (tt0) cc_final: 0.6911 (pp20) REVERT: B 65 PHE cc_start: 0.7092 (m-80) cc_final: 0.6266 (m-10) REVERT: B 208 THR cc_start: 0.8500 (m) cc_final: 0.8131 (p) REVERT: B 553 THR cc_start: 0.7389 (p) cc_final: 0.7144 (p) REVERT: B 869 MET cc_start: 0.7681 (mtm) cc_final: 0.7433 (mtm) REVERT: C 580 GLN cc_start: 0.6737 (tp40) cc_final: 0.6250 (mt0) REVERT: H 83 MET cc_start: 0.4136 (ptp) cc_final: 0.3450 (ptm) REVERT: H 230 LYS cc_start: -0.0559 (tttt) cc_final: -0.1852 (tppt) outliers start: 14 outliers final: 4 residues processed: 419 average time/residue: 0.4423 time to fit residues: 303.0190 Evaluate side-chains 258 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 254 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain H residue 84 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 20.0000 chunk 312 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 374 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 762 GLN A 949 GLN A 969 ASN A1142 GLN B 164 ASN B 644 GLN B 954 GLN C 30 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C1088 HIS F 35 HIS ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS H 104 HIS ** H 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 ASN L 198 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33844 Z= 0.313 Angle : 0.623 10.985 46091 Z= 0.323 Chirality : 0.046 0.360 5373 Planarity : 0.005 0.064 5894 Dihedral : 7.266 59.151 5714 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 4.64 % Allowed : 21.55 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.49 (0.13), residues: 4122 helix: 1.34 (0.20), residues: 677 sheet: -0.33 (0.16), residues: 1058 loop : -0.79 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 886 HIS 0.012 0.001 HIS H 104 PHE 0.024 0.002 PHE A 168 TYR 0.022 0.002 TYR C 904 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 266 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7491 (mttt) cc_final: 0.7272 (tttp) REVERT: A 133 PHE cc_start: 0.7551 (m-80) cc_final: 0.6441 (m-80) REVERT: A 275 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8547 (m-10) REVERT: A 380 TYR cc_start: 0.7466 (m-10) cc_final: 0.7164 (m-10) REVERT: A 514 SER cc_start: 0.7467 (OUTLIER) cc_final: 0.7154 (p) REVERT: A 544 ASN cc_start: 0.7939 (t0) cc_final: 0.7146 (p0) REVERT: A 950 ASP cc_start: 0.8406 (t0) cc_final: 0.7986 (t0) REVERT: A 978 ASN cc_start: 0.7051 (m-40) cc_final: 0.6840 (t0) REVERT: A 990 GLU cc_start: 0.7380 (tt0) cc_final: 0.6938 (pp20) REVERT: B 51 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8737 (p) REVERT: B 65 PHE cc_start: 0.6800 (m-80) cc_final: 0.6403 (m-10) REVERT: B 81 ASN cc_start: 0.8163 (p0) cc_final: 0.7951 (p0) REVERT: B 83 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7669 (p) REVERT: B 189 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8342 (tt) REVERT: B 270 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7928 (mp) REVERT: C 36 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7048 (p) REVERT: C 99 ASN cc_start: 0.6464 (OUTLIER) cc_final: 0.5862 (t0) REVERT: C 377 PHE cc_start: 0.5490 (OUTLIER) cc_final: 0.5194 (p90) REVERT: C 580 GLN cc_start: 0.6807 (tp40) cc_final: 0.6282 (mt0) REVERT: C 868 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6451 (tm-30) REVERT: C 1104 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8321 (p) REVERT: C 1144 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7634 (tm-30) REVERT: H 83 MET cc_start: 0.4036 (ptp) cc_final: 0.3174 (ptm) REVERT: H 118 TYR cc_start: 0.3686 (t80) cc_final: 0.3350 (t80) REVERT: H 230 LYS cc_start: -0.0649 (tttt) cc_final: -0.1889 (tppt) outliers start: 168 outliers final: 97 residues processed: 417 average time/residue: 0.4068 time to fit residues: 286.6065 Evaluate side-chains 328 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 221 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 22 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 311 optimal weight: 0.6980 chunk 254 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 374 optimal weight: 20.0000 chunk 404 optimal weight: 8.9990 chunk 333 optimal weight: 8.9990 chunk 371 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 300 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN A 121 ASN A 271 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 954 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 HIS F 77 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33844 Z= 0.256 Angle : 0.569 9.735 46091 Z= 0.294 Chirality : 0.045 0.355 5373 Planarity : 0.004 0.076 5894 Dihedral : 6.797 58.630 5714 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.83 % Rotamer: Outliers : 5.19 % Allowed : 21.17 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.52 (0.13), residues: 4122 helix: 1.21 (0.20), residues: 676 sheet: -0.31 (0.16), residues: 1046 loop : -0.80 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 886 HIS 0.006 0.001 HIS H 104 PHE 0.027 0.001 PHE C 65 TYR 0.020 0.001 TYR B1067 ARG 0.006 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 226 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7967 (tp40) cc_final: 0.7278 (tp40) REVERT: A 84 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6882 (mm) REVERT: A 129 LYS cc_start: 0.7428 (mttt) cc_final: 0.7148 (ttmp) REVERT: A 133 PHE cc_start: 0.7522 (m-80) cc_final: 0.6365 (m-80) REVERT: A 370 ASN cc_start: 0.8530 (p0) cc_final: 0.8313 (p0) REVERT: A 544 ASN cc_start: 0.7960 (t0) cc_final: 0.7148 (p0) REVERT: A 740 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8040 (tmm) REVERT: A 978 ASN cc_start: 0.7051 (m-40) cc_final: 0.6839 (t0) REVERT: A 990 GLU cc_start: 0.7378 (tt0) cc_final: 0.6916 (pp20) REVERT: B 51 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8696 (p) REVERT: B 65 PHE cc_start: 0.6797 (m-80) cc_final: 0.6210 (m-10) REVERT: B 83 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7688 (p) REVERT: B 238 PHE cc_start: 0.5784 (OUTLIER) cc_final: 0.4944 (p90) REVERT: C 99 ASN cc_start: 0.6344 (OUTLIER) cc_final: 0.5959 (t0) REVERT: C 580 GLN cc_start: 0.6682 (tp40) cc_final: 0.6094 (mt0) REVERT: C 868 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6435 (tm-30) REVERT: C 869 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8147 (mtt) REVERT: C 933 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8221 (ttpt) REVERT: C 987 PRO cc_start: 0.8731 (OUTLIER) cc_final: 0.8500 (Cg_endo) REVERT: C 1144 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7640 (tm-30) REVERT: H 83 MET cc_start: 0.3769 (ptp) cc_final: 0.2920 (ptm) REVERT: H 119 TRP cc_start: 0.1564 (OUTLIER) cc_final: 0.0930 (m-10) REVERT: H 123 THR cc_start: 0.1957 (OUTLIER) cc_final: 0.1573 (t) REVERT: H 230 LYS cc_start: -0.0754 (tttt) cc_final: -0.1976 (tppt) outliers start: 188 outliers final: 126 residues processed: 391 average time/residue: 0.3886 time to fit residues: 260.1467 Evaluate side-chains 342 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 206 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 119 TRP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 20.0000 chunk 281 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 251 optimal weight: 20.0000 chunk 376 optimal weight: 9.9990 chunk 398 optimal weight: 9.9990 chunk 196 optimal weight: 0.9990 chunk 356 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33844 Z= 0.263 Angle : 0.565 9.466 46091 Z= 0.290 Chirality : 0.045 0.352 5373 Planarity : 0.004 0.076 5894 Dihedral : 6.478 57.429 5714 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.83 % Rotamer: Outliers : 6.00 % Allowed : 20.72 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.56 (0.13), residues: 4122 helix: 1.13 (0.20), residues: 682 sheet: -0.34 (0.16), residues: 1051 loop : -0.81 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 886 HIS 0.009 0.001 HIS A 207 PHE 0.021 0.001 PHE A 135 TYR 0.029 0.001 TYR L 37 ARG 0.006 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 219 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7970 (tp40) cc_final: 0.7298 (tp40) REVERT: A 84 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7033 (mm) REVERT: A 133 PHE cc_start: 0.7407 (m-80) cc_final: 0.6463 (m-80) REVERT: A 306 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: A 544 ASN cc_start: 0.8030 (t0) cc_final: 0.7258 (p0) REVERT: A 740 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8077 (tmm) REVERT: A 779 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 978 ASN cc_start: 0.7091 (m-40) cc_final: 0.6841 (t0) REVERT: A 990 GLU cc_start: 0.7396 (tt0) cc_final: 0.6896 (pp20) REVERT: A 1051 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8564 (p) REVERT: B 51 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8650 (p) REVERT: B 65 PHE cc_start: 0.6772 (m-80) cc_final: 0.6189 (m-10) REVERT: B 238 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5125 (p90) REVERT: B 270 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8017 (mp) REVERT: B 611 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7979 (tp) REVERT: B 1002 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: C 36 VAL cc_start: 0.7322 (OUTLIER) cc_final: 0.6903 (p) REVERT: C 99 ASN cc_start: 0.6298 (OUTLIER) cc_final: 0.5965 (t0) REVERT: C 580 GLN cc_start: 0.6624 (tp40) cc_final: 0.6000 (mt0) REVERT: C 662 CYS cc_start: 0.8414 (t) cc_final: 0.8101 (t) REVERT: C 698 SER cc_start: 0.8883 (t) cc_final: 0.8490 (p) REVERT: C 933 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8267 (ttpt) REVERT: C 987 PRO cc_start: 0.8732 (OUTLIER) cc_final: 0.8496 (Cg_endo) REVERT: C 1072 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: C 1144 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7719 (tm-30) REVERT: H 83 MET cc_start: 0.3501 (ptp) cc_final: 0.2708 (ptm) REVERT: H 119 TRP cc_start: 0.1358 (m100) cc_final: 0.0568 (m100) REVERT: H 230 LYS cc_start: -0.0848 (tttt) cc_final: -0.2083 (tppt) outliers start: 217 outliers final: 157 residues processed: 411 average time/residue: 0.4185 time to fit residues: 289.7204 Evaluate side-chains 376 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 206 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 339 optimal weight: 20.0000 chunk 275 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 203 optimal weight: 0.7980 chunk 357 optimal weight: 50.0000 chunk 100 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33844 Z= 0.234 Angle : 0.546 8.740 46091 Z= 0.279 Chirality : 0.044 0.354 5373 Planarity : 0.004 0.075 5894 Dihedral : 6.257 58.148 5712 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 5.58 % Allowed : 21.53 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.50 (0.13), residues: 4122 helix: 1.23 (0.20), residues: 676 sheet: -0.26 (0.16), residues: 1054 loop : -0.81 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.004 0.001 HIS H 104 PHE 0.021 0.001 PHE A 135 TYR 0.024 0.001 TYR A 904 ARG 0.004 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 214 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7968 (tp40) cc_final: 0.7281 (tp40) REVERT: A 84 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7088 (mm) REVERT: A 133 PHE cc_start: 0.7356 (m-80) cc_final: 0.6419 (m-80) REVERT: A 306 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: A 454 ARG cc_start: 0.6401 (ttm-80) cc_final: 0.6141 (tpp80) REVERT: A 544 ASN cc_start: 0.8066 (t0) cc_final: 0.7228 (p0) REVERT: A 740 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8046 (tmm) REVERT: A 779 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 978 ASN cc_start: 0.7086 (m-40) cc_final: 0.6829 (t0) REVERT: A 990 GLU cc_start: 0.7391 (tt0) cc_final: 0.6864 (pp20) REVERT: A 1034 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 1051 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8578 (p) REVERT: B 51 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 53 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6807 (m-30) REVERT: B 65 PHE cc_start: 0.6755 (m-80) cc_final: 0.6040 (m-10) REVERT: B 238 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5109 (p90) REVERT: B 580 GLN cc_start: 0.8489 (tt0) cc_final: 0.8255 (mt0) REVERT: B 583 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 611 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7966 (tp) REVERT: B 869 MET cc_start: 0.7582 (mtm) cc_final: 0.7344 (mtm) REVERT: B 873 TYR cc_start: 0.8374 (m-80) cc_final: 0.8104 (m-80) REVERT: B 1002 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: C 580 GLN cc_start: 0.6637 (tp40) cc_final: 0.5971 (mt0) REVERT: C 662 CYS cc_start: 0.8403 (t) cc_final: 0.8101 (t) REVERT: C 698 SER cc_start: 0.8844 (t) cc_final: 0.8412 (p) REVERT: C 933 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8241 (ttpt) REVERT: C 987 PRO cc_start: 0.8732 (OUTLIER) cc_final: 0.8493 (Cg_endo) REVERT: C 1072 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8446 (pm20) REVERT: C 1144 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7716 (tm-30) REVERT: G 78 ILE cc_start: -0.2587 (OUTLIER) cc_final: -0.2981 (tp) REVERT: H 43 LYS cc_start: 0.1331 (tptp) cc_final: 0.0871 (tptm) REVERT: H 83 MET cc_start: 0.3209 (ptp) cc_final: 0.2590 (ptm) REVERT: H 230 LYS cc_start: -0.1040 (tttt) cc_final: -0.2225 (tppt) outliers start: 202 outliers final: 157 residues processed: 392 average time/residue: 0.3973 time to fit residues: 268.2397 Evaluate side-chains 374 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 204 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 0.8980 chunk 358 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 233 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 398 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 184 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 131 optimal weight: 0.0370 chunk 209 optimal weight: 1.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5712 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33844 Z= 0.162 Angle : 0.518 11.735 46091 Z= 0.262 Chirality : 0.043 0.352 5373 Planarity : 0.004 0.074 5894 Dihedral : 5.969 59.516 5712 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 4.53 % Allowed : 22.33 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.36 (0.13), residues: 4122 helix: 1.38 (0.21), residues: 683 sheet: -0.15 (0.16), residues: 1065 loop : -0.74 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 47 HIS 0.004 0.001 HIS C1048 PHE 0.022 0.001 PHE A 135 TYR 0.026 0.001 TYR A 904 ARG 0.016 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 228 time to evaluate : 3.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7965 (tp40) cc_final: 0.7257 (tp40) REVERT: A 133 PHE cc_start: 0.7309 (m-80) cc_final: 0.6399 (m-80) REVERT: A 306 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: A 452 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8289 (tp) REVERT: A 544 ASN cc_start: 0.8053 (t0) cc_final: 0.7258 (p0) REVERT: A 614 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7920 (p0) REVERT: A 740 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8015 (tmm) REVERT: A 779 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 978 ASN cc_start: 0.7106 (m-40) cc_final: 0.6806 (t0) REVERT: A 990 GLU cc_start: 0.7365 (tt0) cc_final: 0.6855 (pp20) REVERT: B 51 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8580 (p) REVERT: B 65 PHE cc_start: 0.6599 (m-80) cc_final: 0.5809 (m-10) REVERT: B 238 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.4981 (p90) REVERT: B 583 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 611 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7903 (tp) REVERT: B 820 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7701 (t0) REVERT: B 1002 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: C 302 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8212 (t) REVERT: C 580 GLN cc_start: 0.6504 (tp40) cc_final: 0.5826 (mt0) REVERT: C 662 CYS cc_start: 0.8367 (t) cc_final: 0.8044 (t) REVERT: C 698 SER cc_start: 0.8646 (t) cc_final: 0.8431 (p) REVERT: C 933 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8163 (ttpt) REVERT: C 987 PRO cc_start: 0.8716 (OUTLIER) cc_final: 0.8482 (Cg_endo) REVERT: C 1072 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8391 (pm20) REVERT: C 1144 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7712 (tm-30) REVERT: G 95 ASP cc_start: -0.2668 (OUTLIER) cc_final: -0.3104 (p0) REVERT: H 43 LYS cc_start: 0.1401 (tptp) cc_final: 0.1092 (tptm) REVERT: H 83 MET cc_start: 0.3222 (ptp) cc_final: 0.2579 (ptm) REVERT: H 230 LYS cc_start: -0.1085 (tttt) cc_final: -0.2188 (tppt) outliers start: 164 outliers final: 118 residues processed: 367 average time/residue: 0.4004 time to fit residues: 251.3890 Evaluate side-chains 335 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 204 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 291 optimal weight: 0.0980 chunk 225 optimal weight: 6.9990 chunk 335 optimal weight: 20.0000 chunk 222 optimal weight: 0.6980 chunk 397 optimal weight: 40.0000 chunk 248 optimal weight: 2.9990 chunk 242 optimal weight: 0.6980 chunk 183 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33844 Z= 0.213 Angle : 0.536 11.368 46091 Z= 0.271 Chirality : 0.044 0.352 5373 Planarity : 0.004 0.075 5894 Dihedral : 5.909 59.636 5711 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.08 % Allowed : 21.97 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.38 (0.13), residues: 4122 helix: 1.40 (0.21), residues: 669 sheet: -0.18 (0.16), residues: 1055 loop : -0.74 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.009 0.001 HIS H 104 PHE 0.021 0.001 PHE C 65 TYR 0.029 0.001 TYR A 904 ARG 0.008 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 211 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7981 (tp40) cc_final: 0.7269 (tp40) REVERT: A 133 PHE cc_start: 0.7447 (m-80) cc_final: 0.6549 (m-80) REVERT: A 306 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: A 452 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8282 (tp) REVERT: A 544 ASN cc_start: 0.8079 (t0) cc_final: 0.7286 (p0) REVERT: A 614 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7915 (p0) REVERT: A 740 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8023 (tmm) REVERT: A 779 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 978 ASN cc_start: 0.6995 (m-40) cc_final: 0.6762 (t0) REVERT: A 990 GLU cc_start: 0.7403 (tt0) cc_final: 0.6853 (pp20) REVERT: A 1034 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8287 (mp) REVERT: B 51 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8605 (p) REVERT: B 65 PHE cc_start: 0.6577 (m-80) cc_final: 0.5878 (m-10) REVERT: B 238 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5166 (p90) REVERT: B 583 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 611 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7901 (tp) REVERT: B 1002 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: C 117 LEU cc_start: 0.7620 (mp) cc_final: 0.7409 (tt) REVERT: C 580 GLN cc_start: 0.6528 (tp40) cc_final: 0.5811 (mt0) REVERT: C 662 CYS cc_start: 0.8447 (t) cc_final: 0.8091 (t) REVERT: C 698 SER cc_start: 0.8818 (t) cc_final: 0.8357 (p) REVERT: C 933 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8189 (ttpt) REVERT: C 987 PRO cc_start: 0.8703 (OUTLIER) cc_final: 0.8464 (Cg_endo) REVERT: C 1072 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: C 1144 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7715 (tm-30) REVERT: G 78 ILE cc_start: -0.2590 (OUTLIER) cc_final: -0.3053 (tp) REVERT: G 95 ASP cc_start: -0.1973 (OUTLIER) cc_final: -0.2570 (p0) REVERT: H 43 LYS cc_start: 0.1376 (tptp) cc_final: 0.1026 (tptm) REVERT: H 83 MET cc_start: 0.3231 (ptp) cc_final: 0.2607 (ptm) REVERT: H 230 LYS cc_start: -0.1005 (tttt) cc_final: -0.2144 (tppt) outliers start: 184 outliers final: 149 residues processed: 369 average time/residue: 0.3918 time to fit residues: 250.9695 Evaluate side-chains 367 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 205 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 0.6980 chunk 158 optimal weight: 8.9990 chunk 237 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 0.0170 chunk 252 optimal weight: 8.9990 chunk 270 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 312 optimal weight: 0.6980 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33844 Z= 0.221 Angle : 0.539 10.091 46091 Z= 0.274 Chirality : 0.044 0.351 5373 Planarity : 0.004 0.075 5894 Dihedral : 5.862 59.957 5711 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.42 % Allowed : 21.64 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.39 (0.13), residues: 4122 helix: 1.36 (0.21), residues: 669 sheet: -0.19 (0.16), residues: 1078 loop : -0.74 (0.12), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 47 HIS 0.005 0.001 HIS H 104 PHE 0.024 0.001 PHE A 135 TYR 0.032 0.001 TYR A 904 ARG 0.008 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 210 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7986 (tp40) cc_final: 0.7263 (tp40) REVERT: A 133 PHE cc_start: 0.7325 (m-80) cc_final: 0.6439 (m-80) REVERT: A 306 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: A 452 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8278 (tp) REVERT: A 544 ASN cc_start: 0.8105 (t0) cc_final: 0.7285 (p0) REVERT: A 614 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7905 (p0) REVERT: A 740 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8035 (tmm) REVERT: A 779 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 786 LYS cc_start: 0.8204 (pttm) cc_final: 0.7924 (mmmt) REVERT: A 978 ASN cc_start: 0.7012 (m-40) cc_final: 0.6767 (t0) REVERT: A 990 GLU cc_start: 0.7419 (tt0) cc_final: 0.6865 (pp20) REVERT: B 51 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 65 PHE cc_start: 0.6655 (m-80) cc_final: 0.5941 (m-10) REVERT: B 238 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5170 (p90) REVERT: B 270 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7996 (mp) REVERT: B 611 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7885 (tp) REVERT: B 873 TYR cc_start: 0.8388 (m-80) cc_final: 0.8130 (m-10) REVERT: B 1002 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: C 117 LEU cc_start: 0.7664 (mp) cc_final: 0.7393 (tt) REVERT: C 306 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: C 580 GLN cc_start: 0.6520 (tp40) cc_final: 0.5805 (mt0) REVERT: C 662 CYS cc_start: 0.8368 (t) cc_final: 0.8068 (t) REVERT: C 698 SER cc_start: 0.8692 (t) cc_final: 0.8239 (p) REVERT: C 933 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8185 (ttpt) REVERT: C 987 PRO cc_start: 0.8704 (OUTLIER) cc_final: 0.8452 (Cg_endo) REVERT: C 1072 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: C 1144 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7716 (tm-30) REVERT: G 78 ILE cc_start: -0.2425 (OUTLIER) cc_final: -0.2909 (tp) REVERT: G 95 ASP cc_start: -0.2011 (OUTLIER) cc_final: -0.2584 (p0) REVERT: H 43 LYS cc_start: 0.1459 (tptp) cc_final: 0.1052 (tptm) REVERT: H 83 MET cc_start: 0.3333 (ptp) cc_final: 0.2707 (ptm) REVERT: H 230 LYS cc_start: -0.1054 (tttt) cc_final: -0.2164 (tppt) outliers start: 196 outliers final: 162 residues processed: 380 average time/residue: 0.3890 time to fit residues: 254.7329 Evaluate side-chains 376 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 200 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 30.0000 chunk 380 optimal weight: 7.9990 chunk 347 optimal weight: 30.0000 chunk 370 optimal weight: 0.3980 chunk 222 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 290 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 334 optimal weight: 30.0000 chunk 349 optimal weight: 7.9990 chunk 368 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 33844 Z= 0.312 Angle : 0.584 10.968 46091 Z= 0.298 Chirality : 0.045 0.355 5373 Planarity : 0.004 0.075 5894 Dihedral : 6.002 57.292 5711 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.47 % Allowed : 21.72 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.52 (0.13), residues: 4122 helix: 1.08 (0.20), residues: 682 sheet: -0.23 (0.16), residues: 1079 loop : -0.81 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.019 0.001 HIS H 104 PHE 0.024 0.002 PHE A 135 TYR 0.040 0.001 TYR A 904 ARG 0.007 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 194 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7957 (tp40) cc_final: 0.7257 (tp40) REVERT: A 133 PHE cc_start: 0.7326 (m-80) cc_final: 0.6449 (m-80) REVERT: A 306 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: A 452 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8186 (tp) REVERT: A 544 ASN cc_start: 0.8176 (t0) cc_final: 0.7347 (p0) REVERT: A 614 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7908 (p0) REVERT: A 740 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8056 (tmm) REVERT: A 786 LYS cc_start: 0.8245 (pttm) cc_final: 0.7958 (mmmt) REVERT: A 978 ASN cc_start: 0.6979 (m-40) cc_final: 0.6713 (t0) REVERT: A 990 GLU cc_start: 0.7540 (tt0) cc_final: 0.6990 (pp20) REVERT: B 51 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8654 (p) REVERT: B 65 PHE cc_start: 0.6790 (m-80) cc_final: 0.6085 (m-10) REVERT: B 238 PHE cc_start: 0.6187 (OUTLIER) cc_final: 0.5239 (p90) REVERT: B 270 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8025 (mp) REVERT: B 611 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7956 (tp) REVERT: B 1002 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: C 117 LEU cc_start: 0.7622 (mp) cc_final: 0.7352 (tt) REVERT: C 306 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: C 580 GLN cc_start: 0.6580 (tp40) cc_final: 0.5759 (mt0) REVERT: C 662 CYS cc_start: 0.8518 (t) cc_final: 0.8166 (t) REVERT: C 933 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8245 (ttpt) REVERT: C 959 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8121 (mp) REVERT: C 987 PRO cc_start: 0.8705 (OUTLIER) cc_final: 0.8463 (Cg_endo) REVERT: C 1072 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: C 1144 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7722 (tm-30) REVERT: G 78 ILE cc_start: -0.2425 (OUTLIER) cc_final: -0.2928 (tp) REVERT: G 95 ASP cc_start: -0.1833 (OUTLIER) cc_final: -0.2437 (p0) REVERT: H 43 LYS cc_start: 0.1667 (tptp) cc_final: 0.1341 (tptm) REVERT: H 83 MET cc_start: 0.3388 (ptp) cc_final: 0.2686 (ptm) REVERT: H 230 LYS cc_start: -0.0934 (tttt) cc_final: -0.2095 (tppt) outliers start: 198 outliers final: 161 residues processed: 372 average time/residue: 0.3947 time to fit residues: 256.2430 Evaluate side-chains 362 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 186 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 0.2980 chunk 391 optimal weight: 30.0000 chunk 238 optimal weight: 5.9990 chunk 185 optimal weight: 0.4980 chunk 272 optimal weight: 0.9990 chunk 410 optimal weight: 20.0000 chunk 377 optimal weight: 30.0000 chunk 326 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33844 Z= 0.262 Angle : 0.564 10.979 46091 Z= 0.286 Chirality : 0.045 0.354 5373 Planarity : 0.004 0.075 5894 Dihedral : 5.969 57.099 5711 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.95 % Allowed : 22.16 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.54 (0.13), residues: 4122 helix: 1.07 (0.20), residues: 687 sheet: -0.22 (0.16), residues: 1072 loop : -0.84 (0.12), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.016 0.001 HIS H 104 PHE 0.025 0.001 PHE A 135 TYR 0.040 0.001 TYR A 904 ARG 0.007 0.000 ARG C 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 195 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7976 (tp40) cc_final: 0.7266 (tp40) REVERT: A 133 PHE cc_start: 0.7331 (m-80) cc_final: 0.6475 (m-80) REVERT: A 306 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: A 452 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8172 (tp) REVERT: A 544 ASN cc_start: 0.8181 (t0) cc_final: 0.7343 (p0) REVERT: A 614 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7905 (p0) REVERT: A 740 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8034 (tmm) REVERT: A 786 LYS cc_start: 0.8245 (pttm) cc_final: 0.7910 (mmmt) REVERT: A 978 ASN cc_start: 0.6982 (m-40) cc_final: 0.6712 (t0) REVERT: A 990 GLU cc_start: 0.7521 (tt0) cc_final: 0.6971 (pp20) REVERT: B 65 PHE cc_start: 0.6764 (m-80) cc_final: 0.6054 (m-10) REVERT: B 238 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.5203 (p90) REVERT: B 270 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 611 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7987 (tp) REVERT: B 873 TYR cc_start: 0.8369 (m-80) cc_final: 0.8147 (m-10) REVERT: B 1002 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: C 117 LEU cc_start: 0.7612 (mp) cc_final: 0.7326 (tt) REVERT: C 306 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: C 314 GLN cc_start: 0.7865 (pm20) cc_final: 0.7552 (pm20) REVERT: C 580 GLN cc_start: 0.6563 (tp40) cc_final: 0.5733 (mt0) REVERT: C 662 CYS cc_start: 0.8444 (t) cc_final: 0.8122 (t) REVERT: C 904 TYR cc_start: 0.7332 (t80) cc_final: 0.7006 (t80) REVERT: C 933 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8224 (ttpt) REVERT: C 987 PRO cc_start: 0.8695 (OUTLIER) cc_final: 0.8451 (Cg_endo) REVERT: C 1072 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8495 (pm20) REVERT: C 1144 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7726 (tm-30) REVERT: G 78 ILE cc_start: -0.2421 (OUTLIER) cc_final: -0.2920 (tp) REVERT: G 95 ASP cc_start: -0.1751 (OUTLIER) cc_final: -0.2418 (p0) REVERT: H 34 MET cc_start: 0.4995 (ptp) cc_final: 0.4750 (ptm) REVERT: H 43 LYS cc_start: 0.1759 (tptp) cc_final: 0.1370 (tptm) REVERT: H 83 MET cc_start: 0.3450 (ptp) cc_final: 0.2779 (ptm) REVERT: H 230 LYS cc_start: -0.0979 (tttt) cc_final: -0.2136 (tppt) outliers start: 179 outliers final: 161 residues processed: 358 average time/residue: 0.4006 time to fit residues: 247.4776 Evaluate side-chains 365 residues out of total 3620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 191 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 259 optimal weight: 20.0000 chunk 348 optimal weight: 0.1980 chunk 100 optimal weight: 0.5980 chunk 301 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 327 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 336 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 271 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.228178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.184515 restraints weight = 56623.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.177249 restraints weight = 73947.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.173416 restraints weight = 61685.391| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33844 Z= 0.199 Angle : 0.540 11.150 46091 Z= 0.272 Chirality : 0.044 0.351 5373 Planarity : 0.004 0.074 5894 Dihedral : 5.870 58.252 5711 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.70 % Allowed : 22.55 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.64 % 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: -0.45 (0.13), residues: 4122 helix: 1.20 (0.20), residues: 688 sheet: -0.17 (0.16), residues: 1067 loop : -0.80 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.006 0.001 HIS H 104 PHE 0.025 0.001 PHE A 135 TYR 0.036 0.001 TYR A 904 ARG 0.007 0.000 ARG C 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6479.68 seconds wall clock time: 119 minutes 45.06 seconds (7185.06 seconds total)