Starting phenix.real_space_refine on Tue Feb 20 02:42:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiw_33210/02_2024/7xiw_33210.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiw_33210/02_2024/7xiw_33210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiw_33210/02_2024/7xiw_33210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiw_33210/02_2024/7xiw_33210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiw_33210/02_2024/7xiw_33210.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiw_33210/02_2024/7xiw_33210.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.063 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 112 5.16 5 C 16971 2.51 5 N 4358 2.21 5 O 5183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 773": "OE1" <-> "OE2" Residue "D TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26624 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8610 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8604 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1043} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 8626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8626 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1046} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" 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: 13.95, per 1000 atoms: 0.52 Number of scatterers: 26624 At special positions: 0 Unit cell: (157.29, 153.01, 206.51, 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 112 16.00 O 5183 8.00 N 4358 7.00 C 16971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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 C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C 1 " - " ASN A 343 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 165 " " NAG D1304 " - " ASN D 234 " " NAG D1305 " - " ASN D 282 " " NAG D1306 " - " ASN D 616 " " NAG D1307 " - " ASN D 657 " " NAG D1308 " - " ASN D 709 " " NAG D1309 " - " ASN D 801 " " NAG D1311 " - " ASN D1074 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 343 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN D 717 " " NAG O 1 " - " ASN D1098 " " NAG P 1 " - " ASN D1134 " Time building additional restraints: 10.01 Conformation dependent library (CDL) restraints added in 5.0 seconds 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 49 sheets defined 22.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.086A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.170A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.670A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.709A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.559A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 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 762 through 783 removed outlier: 3.749A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.505A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.681A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.587A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.765A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.716A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.544A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.206A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1150 removed outlier: 3.780A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.932A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.610A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 765 through 783 removed outlier: 3.860A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.773A pdb=" N LYS B 854 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.861A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 933 Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.593A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.589A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.344A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1150 removed outlier: 3.963A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.780A pdb=" N ASN D 370 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA D 372 " --> pdb=" O TYR D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 760 through 783 removed outlier: 3.893A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 849 through 854 removed outlier: 3.885A pdb=" N LYS D 854 " --> pdb=" O CYS D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.735A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.719A pdb=" N LYS D 933 " --> pdb=" O SER D 929 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.580A pdb=" N GLN D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN D 955 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 956 " --> pdb=" O VAL D 952 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 957 " --> pdb=" O ASN D 953 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA D 958 " --> pdb=" O HIS D 954 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.242A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D1007 " --> pdb=" O SER D1003 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D1013 " --> pdb=" O THR D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1150 removed outlier: 3.932A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D1148 " --> pdb=" O GLU D1144 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D1150 " --> pdb=" O ASP D1146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 31 removed outlier: 3.605A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.621A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 4.278A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 4.278A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.600A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.371A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.371A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.238A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 6.906A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.828A pdb=" N VAL A 656 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 722 removed outlier: 6.492A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 722 removed outlier: 6.492A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.855A pdb=" N ILE A 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.599A pdb=" N SER B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.558A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.842A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.842A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.559A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.593A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.005A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.824A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.824A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 659 through 660 removed outlier: 4.196A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.543A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.618A pdb=" N THR D 29 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 63 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 193 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 51 through 55 removed outlier: 3.595A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 116 through 117 Processing sheet with id=AE1, first strand: chain 'D' and resid 120 through 121 Processing sheet with id=AE2, first strand: chain 'D' and resid 278 through 279 removed outlier: 3.941A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 311 through 312 removed outlier: 4.178A pdb=" N PHE D 318 " --> pdb=" O GLY D 593 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 311 through 312 removed outlier: 3.819A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 650 " --> pdb=" O PHE D 643 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 325 through 327 removed outlier: 6.884A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 550 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.683A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 378 through 379 removed outlier: 3.834A pdb=" N CYS D 432 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE D 402 " --> pdb=" O TYR D 508 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL D 510 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE D 400 " --> pdb=" O VAL D 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.145A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 712 through 719 removed outlier: 6.440A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 722 through 728 removed outlier: 3.635A pdb=" N GLY D1059 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 1094 through 1097 771 hydrogen bonds defined for protein. 2073 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: 11.66 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8454 1.35 - 1.47: 6930 1.47 - 1.59: 11734 1.59 - 1.71: 0 1.71 - 1.83: 140 Bond restraints: 27258 Sorted by residual: bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" N PHE D 157 " pdb=" CA PHE D 157 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.20e+00 bond pdb=" CB PRO A 373 " pdb=" CG PRO A 373 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.02e+00 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.86e+00 ... (remaining 27253 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.50: 777 106.50 - 113.38: 14870 113.38 - 120.27: 9231 120.27 - 127.15: 11987 127.15 - 134.04: 255 Bond angle restraints: 37120 Sorted by residual: angle pdb=" C GLY B 232 " pdb=" N ILE B 233 " pdb=" CA ILE B 233 " ideal model delta sigma weight residual 121.97 128.61 -6.64 1.80e+00 3.09e-01 1.36e+01 angle pdb=" N GLY A 757 " pdb=" CA GLY A 757 " pdb=" C GLY A 757 " ideal model delta sigma weight residual 111.35 115.48 -4.13 1.20e+00 6.94e-01 1.18e+01 angle pdb=" OG1 THR A 95 " pdb=" CB THR A 95 " pdb=" CG2 THR A 95 " ideal model delta sigma weight residual 109.30 103.29 6.01 2.00e+00 2.50e-01 9.04e+00 angle pdb=" OG1 THR B 547 " pdb=" CB THR B 547 " pdb=" CG2 THR B 547 " ideal model delta sigma weight residual 109.30 103.29 6.01 2.00e+00 2.50e-01 9.04e+00 angle pdb=" N VAL D 620 " pdb=" CA VAL D 620 " pdb=" C VAL D 620 " ideal model delta sigma weight residual 108.88 115.37 -6.49 2.16e+00 2.14e-01 9.02e+00 ... (remaining 37115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15292 17.91 - 35.83: 1256 35.83 - 53.74: 277 53.74 - 71.65: 59 71.65 - 89.57: 31 Dihedral angle restraints: 16915 sinusoidal: 7280 harmonic: 9635 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -10.49 -75.51 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYS D1082 " pdb=" SG CYS D1082 " pdb=" SG CYS D1126 " pdb=" CB CYS D1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.76 71.76 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -16.16 -69.84 1 1.00e+01 1.00e-02 6.29e+01 ... (remaining 16912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3676 0.061 - 0.122: 608 0.122 - 0.183: 43 0.183 - 0.244: 8 0.244 - 0.305: 2 Chirality restraints: 4337 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4334 not shown) Planarity restraints: 4784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 294 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO D 295 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 295 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 295 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 620 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B 621 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 621 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 621 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D1056 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO D1057 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D1057 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D1057 " -0.023 5.00e-02 4.00e+02 ... (remaining 4781 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 2 2.06 - 2.77: 4705 2.77 - 3.48: 34608 3.48 - 4.19: 56099 4.19 - 4.90: 100406 Nonbonded interactions: 195820 Sorted by model distance: nonbonded pdb=" CE MET B 153 " pdb=" CD2 HIS B 245 " model vdw 1.353 3.680 nonbonded pdb=" O ASN B 185 " pdb=" CD2 LEU B 212 " model vdw 1.945 3.460 nonbonded pdb=" O ALA B 67 " pdb=" OG1 THR B 250 " model vdw 2.132 2.440 nonbonded pdb=" OH TYR D 655 " pdb=" OG1 THR D 696 " model vdw 2.184 2.440 nonbonded pdb=" O ALA A 292 " pdb=" OG1 THR A 632 " model vdw 2.191 2.440 ... (remaining 195815 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 25 through 835 or resid 849 through 1150 or resid 1301 thr \ ough 1309)) selection = (chain 'B' and (resid 25 through 152 or (resid 153 and (name N or name CA or nam \ e C or name O or name CB )) or resid 154 through 1150 or resid 1301 through 1309 \ )) selection = (chain 'D' and (resid 25 through 835 or resid 849 through 1150 or resid 1301 thr \ ough 1309)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 2.980 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: 0.020 Extract box with map and model: 8.570 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 70.540 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 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 0.087 27258 Z= 0.213 Angle : 0.589 8.349 37120 Z= 0.297 Chirality : 0.046 0.305 4337 Planarity : 0.004 0.058 4743 Dihedral : 13.911 89.567 10621 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.26 % Favored : 93.35 % Rotamer: Outliers : 0.03 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 3292 helix: 0.96 (0.23), residues: 628 sheet: -0.57 (0.22), residues: 631 loop : -1.62 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.000 HIS B 245 PHE 0.019 0.001 PHE D 65 TYR 0.019 0.001 TYR B 904 ARG 0.005 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 466 time to evaluate : 2.986 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: A 400 PHE cc_start: 0.3809 (p90) cc_final: 0.3601 (p90) outliers start: 1 outliers final: 0 residues processed: 467 average time/residue: 0.4144 time to fit residues: 295.9408 Evaluate side-chains 220 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 258 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 192 optimal weight: 0.8980 chunk 299 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 405 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 613 GLN A 658 ASN A 675 GLN A 751 ASN A 955 ASN A 957 GLN A1071 GLN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1088 HIS D 314 GLN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN D 955 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27258 Z= 0.235 Angle : 0.622 9.851 37120 Z= 0.320 Chirality : 0.046 0.387 4337 Planarity : 0.004 0.056 4743 Dihedral : 7.275 59.938 4730 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.59 % Favored : 93.01 % Rotamer: Outliers : 1.36 % Allowed : 9.62 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 3292 helix: 1.20 (0.22), residues: 637 sheet: -0.72 (0.20), residues: 692 loop : -1.66 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 353 HIS 0.006 0.001 HIS A 207 PHE 0.030 0.002 PHE D 562 TYR 0.026 0.001 TYR A 170 ARG 0.008 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 228 time to evaluate : 2.796 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: A 42 VAL cc_start: 0.8425 (p) cc_final: 0.8152 (p) REVERT: A 54 LEU cc_start: 0.8076 (mt) cc_final: 0.7528 (mp) REVERT: A 1002 GLN cc_start: 0.8211 (tp40) cc_final: 0.7917 (tp40) REVERT: D 119 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7639 (tp) REVERT: D 338 PHE cc_start: 0.7399 (m-10) cc_final: 0.7146 (m-10) REVERT: D 576 VAL cc_start: 0.7284 (OUTLIER) cc_final: 0.6965 (p) REVERT: D 636 TYR cc_start: 0.4963 (p90) cc_final: 0.4760 (p90) outliers start: 39 outliers final: 22 residues processed: 257 average time/residue: 0.3747 time to fit residues: 155.3771 Evaluate side-chains 206 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 182 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 1037 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 7.9990 chunk 93 optimal weight: 0.0170 chunk 249 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 chunk 324 optimal weight: 0.9990 chunk 267 optimal weight: 7.9990 chunk 297 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 901 GLN A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 641 ASN B 762 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27258 Z= 0.215 Angle : 0.582 11.727 37120 Z= 0.296 Chirality : 0.045 0.401 4337 Planarity : 0.004 0.054 4743 Dihedral : 6.468 58.045 4730 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.20 % Favored : 93.41 % Rotamer: Outliers : 2.02 % Allowed : 12.76 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3292 helix: 1.35 (0.22), residues: 640 sheet: -0.71 (0.20), residues: 700 loop : -1.66 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 64 HIS 0.004 0.001 HIS B1083 PHE 0.023 0.002 PHE D 92 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 199 time to evaluate : 3.175 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 1002 GLN cc_start: 0.8069 (tp40) cc_final: 0.7808 (tp40) REVERT: B 398 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6477 (p0) REVERT: D 338 PHE cc_start: 0.7482 (m-10) cc_final: 0.7060 (m-10) REVERT: D 515 PHE cc_start: 0.6783 (m-80) cc_final: 0.6555 (m-80) REVERT: D 576 VAL cc_start: 0.7263 (OUTLIER) cc_final: 0.6914 (p) outliers start: 58 outliers final: 30 residues processed: 245 average time/residue: 0.3900 time to fit residues: 156.1545 Evaluate side-chains 205 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 963 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 0.2980 chunk 225 optimal weight: 0.0470 chunk 155 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 143 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 318 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 285 optimal weight: 0.0070 chunk 85 optimal weight: 3.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 405 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1002 GLN A1005 GLN B 317 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN D 125 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN D1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27258 Z= 0.141 Angle : 0.548 12.838 37120 Z= 0.276 Chirality : 0.044 0.396 4337 Planarity : 0.004 0.053 4743 Dihedral : 6.070 57.959 4730 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.83 % Favored : 93.74 % Rotamer: Outliers : 1.95 % Allowed : 14.36 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3292 helix: 1.59 (0.23), residues: 634 sheet: -0.53 (0.20), residues: 668 loop : -1.59 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 64 HIS 0.002 0.000 HIS B 49 PHE 0.025 0.001 PHE D 562 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 197 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7833 (tp40) REVERT: B 398 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6347 (p0) REVERT: D 119 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7415 (tp) REVERT: D 338 PHE cc_start: 0.7393 (m-10) cc_final: 0.6987 (m-10) REVERT: D 515 PHE cc_start: 0.6829 (m-80) cc_final: 0.6622 (m-80) REVERT: D 576 VAL cc_start: 0.7349 (OUTLIER) cc_final: 0.7042 (p) outliers start: 56 outliers final: 29 residues processed: 234 average time/residue: 0.3627 time to fit residues: 140.5063 Evaluate side-chains 208 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 856 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 20.0000 chunk 181 optimal weight: 0.0060 chunk 4 optimal weight: 0.5980 chunk 237 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 272 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 286 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 overall best weight: 3.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1106 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 613 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 27258 Z= 0.367 Angle : 0.713 13.967 37120 Z= 0.362 Chirality : 0.048 0.417 4337 Planarity : 0.005 0.054 4743 Dihedral : 6.404 59.818 4730 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.41 % Favored : 91.16 % Rotamer: Outliers : 2.89 % Allowed : 15.86 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3292 helix: 1.16 (0.22), residues: 627 sheet: -0.69 (0.20), residues: 681 loop : -1.83 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 152 HIS 0.007 0.002 HIS B 49 PHE 0.030 0.002 PHE B 371 TYR 0.031 0.002 TYR A 266 ARG 0.009 0.001 ARG D 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 185 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 VAL cc_start: 0.6210 (OUTLIER) cc_final: 0.5977 (p) REVERT: B 177 MET cc_start: 0.6499 (mmt) cc_final: 0.6134 (mmp) REVERT: B 398 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6604 (p0) REVERT: D 119 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7280 (tp) REVERT: D 186 PHE cc_start: 0.5824 (m-80) cc_final: 0.5519 (m-80) REVERT: D 338 PHE cc_start: 0.7172 (m-10) cc_final: 0.6754 (m-10) REVERT: D 780 GLU cc_start: 0.7206 (pm20) cc_final: 0.6875 (pt0) outliers start: 83 outliers final: 44 residues processed: 250 average time/residue: 0.3570 time to fit residues: 148.2174 Evaluate side-chains 211 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 164 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.9990 chunk 287 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 187 optimal weight: 0.5980 chunk 78 optimal weight: 0.0980 chunk 319 optimal weight: 2.9990 chunk 265 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 245 HIS A 422 ASN A1119 ASN B 317 ASN B 658 ASN D 125 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27258 Z= 0.166 Angle : 0.575 12.229 37120 Z= 0.290 Chirality : 0.045 0.414 4337 Planarity : 0.004 0.060 4743 Dihedral : 5.822 56.313 4730 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.74 % Favored : 93.83 % Rotamer: Outliers : 1.71 % Allowed : 17.60 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 3292 helix: 1.58 (0.22), residues: 629 sheet: -0.56 (0.20), residues: 690 loop : -1.72 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.002 0.001 HIS B1083 PHE 0.023 0.001 PHE D 92 TYR 0.019 0.001 TYR A1067 ARG 0.007 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 184 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 858 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8786 (mp) REVERT: B 177 MET cc_start: 0.6356 (mmt) cc_final: 0.6031 (mmp) REVERT: B 398 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: B 737 ASP cc_start: 0.6972 (t0) cc_final: 0.6702 (t0) REVERT: D 119 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7186 (tp) REVERT: D 177 MET cc_start: 0.5975 (tmm) cc_final: 0.5763 (tmm) REVERT: D 338 PHE cc_start: 0.7340 (m-10) cc_final: 0.6952 (m-10) REVERT: D 697 MET cc_start: 0.7708 (mmm) cc_final: 0.7497 (mmm) REVERT: D 780 GLU cc_start: 0.6966 (pm20) cc_final: 0.6595 (pt0) outliers start: 49 outliers final: 36 residues processed: 223 average time/residue: 0.3585 time to fit residues: 130.9494 Evaluate side-chains 209 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 170 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 955 ASN Chi-restraints excluded: chain D residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 318 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 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 196 ASN A 405 ASN D 125 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27258 Z= 0.153 Angle : 0.559 13.441 37120 Z= 0.281 Chirality : 0.045 0.407 4337 Planarity : 0.004 0.054 4743 Dihedral : 5.469 57.734 4730 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.65 % Favored : 92.92 % Rotamer: Outliers : 1.99 % Allowed : 17.64 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3292 helix: 1.56 (0.22), residues: 648 sheet: -0.59 (0.20), residues: 707 loop : -1.66 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 64 HIS 0.002 0.001 HIS A 66 PHE 0.019 0.001 PHE B 515 TYR 0.017 0.001 TYR A1067 ARG 0.008 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 179 time to evaluate : 2.940 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 858 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8746 (mp) REVERT: B 153 MET cc_start: 0.4154 (pmm) cc_final: 0.2676 (ptt) REVERT: B 177 MET cc_start: 0.6392 (mmt) cc_final: 0.6061 (mmp) REVERT: B 398 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6495 (p0) REVERT: B 737 ASP cc_start: 0.6951 (t0) cc_final: 0.6712 (t0) REVERT: D 119 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7185 (tp) REVERT: D 177 MET cc_start: 0.6009 (tmm) cc_final: 0.5777 (tmm) REVERT: D 315 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7488 (p) REVERT: D 338 PHE cc_start: 0.7304 (m-10) cc_final: 0.6941 (m-10) outliers start: 57 outliers final: 36 residues processed: 223 average time/residue: 0.3507 time to fit residues: 129.7079 Evaluate side-chains 211 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 171 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 955 ASN Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 157 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 405 ASN A1005 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 613 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27258 Z= 0.230 Angle : 0.599 13.494 37120 Z= 0.303 Chirality : 0.045 0.414 4337 Planarity : 0.004 0.057 4743 Dihedral : 5.525 59.961 4730 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.32 % Favored : 92.22 % Rotamer: Outliers : 2.23 % Allowed : 18.06 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3292 helix: 1.61 (0.22), residues: 639 sheet: -0.50 (0.20), residues: 673 loop : -1.76 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 64 HIS 0.004 0.001 HIS D1058 PHE 0.021 0.001 PHE B 515 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 166 time to evaluate : 2.889 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: A 753 LEU cc_start: 0.9329 (tt) cc_final: 0.9100 (tt) REVERT: A 858 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8789 (mp) REVERT: B 177 MET cc_start: 0.6315 (mmt) cc_final: 0.5988 (mmp) REVERT: B 398 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: D 119 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7077 (tp) REVERT: D 177 MET cc_start: 0.6014 (tmm) cc_final: 0.5810 (tmm) REVERT: D 186 PHE cc_start: 0.6028 (m-80) cc_final: 0.5669 (m-80) REVERT: D 315 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7651 (p) REVERT: D 338 PHE cc_start: 0.7030 (m-10) cc_final: 0.6685 (m-10) REVERT: D 697 MET cc_start: 0.7812 (mmm) cc_final: 0.7558 (mmt) outliers start: 64 outliers final: 43 residues processed: 217 average time/residue: 0.3460 time to fit residues: 125.0496 Evaluate side-chains 208 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 278 optimal weight: 0.7980 chunk 296 optimal weight: 0.0270 chunk 178 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 267 optimal weight: 10.0000 chunk 280 optimal weight: 8.9990 chunk 295 optimal weight: 0.0370 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 580 GLN A 613 GLN A1005 GLN D 125 ASN D 450 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27258 Z= 0.143 Angle : 0.564 14.275 37120 Z= 0.283 Chirality : 0.044 0.413 4337 Planarity : 0.004 0.082 4743 Dihedral : 5.180 56.812 4730 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.08 % Favored : 93.47 % Rotamer: Outliers : 1.67 % Allowed : 18.61 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3292 helix: 1.55 (0.22), residues: 656 sheet: -0.54 (0.19), residues: 718 loop : -1.70 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 64 HIS 0.002 0.000 HIS B 207 PHE 0.017 0.001 PHE B 515 TYR 0.018 0.001 TYR A1067 ARG 0.008 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 176 time to evaluate : 3.296 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: A 753 LEU cc_start: 0.9360 (tt) cc_final: 0.9126 (tt) REVERT: A 858 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8776 (mp) REVERT: B 153 MET cc_start: 0.4465 (pmm) cc_final: 0.2876 (ptt) REVERT: B 177 MET cc_start: 0.6354 (mmt) cc_final: 0.6027 (mmp) REVERT: B 398 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6701 (m-30) REVERT: D 119 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.6926 (tp) REVERT: D 315 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7494 (p) REVERT: D 697 MET cc_start: 0.7759 (mmm) cc_final: 0.7441 (mmm) outliers start: 48 outliers final: 38 residues processed: 213 average time/residue: 0.4240 time to fit residues: 150.1198 Evaluate side-chains 210 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 0.0670 chunk 313 optimal weight: 8.9990 chunk 191 optimal weight: 0.0270 chunk 148 optimal weight: 0.6980 chunk 217 optimal weight: 0.5980 chunk 328 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 261 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 202 optimal weight: 0.0070 chunk 160 optimal weight: 0.7980 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 314 GLN A 405 ASN A 580 GLN A 613 GLN A1005 GLN D 125 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27258 Z= 0.139 Angle : 0.554 15.918 37120 Z= 0.277 Chirality : 0.044 0.397 4337 Planarity : 0.004 0.071 4743 Dihedral : 4.885 57.216 4730 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.74 % Favored : 93.80 % Rotamer: Outliers : 1.74 % Allowed : 18.51 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3292 helix: 1.68 (0.22), residues: 641 sheet: -0.34 (0.20), residues: 674 loop : -1.66 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 64 HIS 0.004 0.000 HIS D 207 PHE 0.028 0.001 PHE D 92 TYR 0.025 0.001 TYR D 904 ARG 0.010 0.000 ARG B1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 181 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5150 (OUTLIER) cc_final: 0.4795 (t0) REVERT: A 858 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8729 (mp) REVERT: A 1002 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7611 (tp40) REVERT: B 153 MET cc_start: 0.4426 (pmm) cc_final: 0.2871 (ptt) REVERT: B 177 MET cc_start: 0.6412 (mmt) cc_final: 0.6112 (mmp) REVERT: B 398 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6492 (p0) REVERT: D 119 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6894 (tp) REVERT: D 177 MET cc_start: 0.5839 (tmm) cc_final: 0.5394 (tpp) REVERT: D 315 THR cc_start: 0.7710 (OUTLIER) cc_final: 0.7474 (p) REVERT: D 515 PHE cc_start: 0.6913 (m-80) cc_final: 0.6687 (m-80) REVERT: D 697 MET cc_start: 0.7852 (mmm) cc_final: 0.7624 (mmt) outliers start: 50 outliers final: 37 residues processed: 218 average time/residue: 0.3741 time to fit residues: 136.6311 Evaluate side-chains 208 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 1.9990 chunk 278 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 241 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 262 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 269 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 613 GLN A1005 GLN D 125 ASN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.131490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.088701 restraints weight = 75632.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091387 restraints weight = 36993.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.093136 restraints weight = 23833.467| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27258 Z= 0.154 Angle : 0.558 11.912 37120 Z= 0.280 Chirality : 0.044 0.403 4337 Planarity : 0.004 0.072 4743 Dihedral : 4.835 58.155 4730 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.38 % Favored : 93.20 % Rotamer: Outliers : 1.67 % Allowed : 19.17 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3292 helix: 1.70 (0.22), residues: 645 sheet: -0.32 (0.20), residues: 676 loop : -1.67 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 64 HIS 0.002 0.000 HIS B1083 PHE 0.019 0.001 PHE B 515 TYR 0.021 0.001 TYR D 904 ARG 0.010 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5035.68 seconds wall clock time: 93 minutes 22.88 seconds (5602.88 seconds total)