Starting phenix.real_space_refine on Fri Feb 23 19:44:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfz_34729/02_2024/8hfz_34729.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfz_34729/02_2024/8hfz_34729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfz_34729/02_2024/8hfz_34729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfz_34729/02_2024/8hfz_34729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfz_34729/02_2024/8hfz_34729.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfz_34729/02_2024/8hfz_34729.pdb" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8986 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 143 5.16 5 C 19538 2.51 5 N 5023 2.21 5 O 5999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 216": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30704 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 8290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8290 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 6 Chain: "B" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8292 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 6 Chain: "C" Number of atoms: 8322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8322 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 58, 'TRANS': 1006} Chain breaks: 6 Chain: "E" Number of atoms: 4889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4889 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 15.60, per 1000 atoms: 0.51 Number of scatterers: 30704 At special positions: 0 Unit cell: (130.9, 146.2, 249.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 143 16.00 O 5999 8.00 N 5023 7.00 C 19538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 616 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG D 1 " - " ASN A 234 " " NAG E 701 " - " ASN E 54 " " NAG E 702 " - " ASN E 432 " " NAG E 703 " - " ASN E 91 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 709 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1074 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 709 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1074 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN E 546 " Time building additional restraints: 12.23 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 704 " pdb="ZN ZN E 704 " - pdb=" ND1 HIS E 378 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 374 " 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7114 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 43 sheets defined 29.6% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.752A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.643A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.652A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 756 No H-bonds generated for 'chain 'A' and resid 754 through 756' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.541A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.738A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.664A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.205A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.745A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.640A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.824A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.273A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.081A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 4.005A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.754A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.667A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.806A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.508A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.869A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.810A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.276A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.273A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.136A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 983 removed outlier: 3.920A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.773A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.488A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 343' Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.724A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.986A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.642A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.577A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.353A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.567A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.920A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.788A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.826A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.189A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 45 removed outlier: 4.252A pdb=" N GLN E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS E 32 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN E 43 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 82 removed outlier: 4.180A pdb=" N MET E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 102 removed outlier: 3.618A pdb=" N LEU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 109 removed outlier: 4.076A pdb=" N VAL E 108 " --> pdb=" O GLY E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 122 removed outlier: 4.027A pdb=" N ARG E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 removed outlier: 4.279A pdb=" N ILE E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.741A pdb=" N GLN E 139 " --> pdb=" O PRO E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.985A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN E 154 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 171 removed outlier: 3.879A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TRP E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 180 removed outlier: 3.592A pdb=" N LEU E 176 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Proline residue: E 178 - end of helix No H-bonds generated for 'chain 'E' and resid 172 through 180' Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 188 through 194 Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 219 through 223 Processing helix chain 'E' and resid 224 through 230 removed outlier: 3.875A pdb=" N ASN E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 229 " --> pdb=" O ASP E 225 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE E 230 " --> pdb=" O VAL E 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 224 through 230' Processing helix chain 'E' and resid 232 through 247 removed outlier: 3.990A pdb=" N LEU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS E 247 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 removed outlier: 3.628A pdb=" N LEU E 267 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 removed outlier: 3.951A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 281 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 283 " --> pdb=" O SER E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 316 removed outlier: 3.519A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 330 removed outlier: 4.524A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.502A pdb=" N PHE E 369 " --> pdb=" O THR E 365 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 376 Processing helix chain 'E' and resid 378 through 382 Processing helix chain 'E' and resid 397 through 405 removed outlier: 4.235A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 407 No H-bonds generated for 'chain 'E' and resid 406 through 407' Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.550A pdb=" N LEU E 418 " --> pdb=" O THR E 414 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA E 420 " --> pdb=" O HIS E 416 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 421 " --> pdb=" O TYR E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 449 removed outlier: 4.253A pdb=" N LEU E 440 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA E 443 " --> pdb=" O LEU E 439 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 446 " --> pdb=" O GLN E 442 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR E 449 " --> pdb=" O THR E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 463 removed outlier: 4.158A pdb=" N GLU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS E 458 " --> pdb=" O TYR E 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL E 463 " --> pdb=" O TRP E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 483 removed outlier: 5.272A pdb=" N MET E 480 " --> pdb=" O TRP E 477 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS E 481 " --> pdb=" O TRP E 478 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG E 482 " --> pdb=" O GLU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 503 removed outlier: 4.047A pdb=" N LEU E 503 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 533 removed outlier: 4.279A pdb=" N THR E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN E 522 " --> pdb=" O ARG E 518 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 554 through 561 removed outlier: 3.814A pdb=" N LEU E 558 " --> pdb=" O LEU E 554 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER E 559 " --> pdb=" O LEU E 555 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 571 removed outlier: 3.657A pdb=" N ALA E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.816A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN E 586 " --> pdb=" O LYS E 582 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 597 removed outlier: 4.030A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.559A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.040A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.695A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.180A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.238A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.637A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.741A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.564A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A1070 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.564A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A1070 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.716A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AB7, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.298A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.813A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.896A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 135 through 141 removed outlier: 7.809A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.287A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.864A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.638A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.028A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.812A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 541 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.545A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.872A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.848A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.848A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.735A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.802A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.550A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.156A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.856A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.025A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.655A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.832A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.652A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.066A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.724A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.433A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1067 hydrogen bonds defined for protein. 2910 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: 12.80 Time building geometry restraints manager: 13.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9707 1.34 - 1.46: 7609 1.46 - 1.58: 13908 1.58 - 1.71: 2 1.71 - 1.83: 191 Bond restraints: 31417 Sorted by residual: bond pdb=" CG PRO E 469 " pdb=" CD PRO E 469 " ideal model delta sigma weight residual 1.503 1.327 0.176 3.40e-02 8.65e+02 2.68e+01 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 31412 not shown) Histogram of bond angle deviations from ideal: 90.72 - 99.42: 5 99.42 - 108.12: 1447 108.12 - 116.81: 20906 116.81 - 125.51: 19953 125.51 - 134.21: 443 Bond angle restraints: 42754 Sorted by residual: angle pdb=" CA PRO E 469 " pdb=" N PRO E 469 " pdb=" CD PRO E 469 " ideal model delta sigma weight residual 112.00 93.14 18.86 1.40e+00 5.10e-01 1.82e+02 angle pdb=" N PRO E 469 " pdb=" CD PRO E 469 " pdb=" CG PRO E 469 " ideal model delta sigma weight residual 103.20 90.72 12.48 1.50e+00 4.44e-01 6.92e+01 angle pdb=" CA PRO E 469 " pdb=" CB PRO E 469 " pdb=" CG PRO E 469 " ideal model delta sigma weight residual 104.50 95.42 9.08 1.90e+00 2.77e-01 2.28e+01 angle pdb=" CA PRO A 25 " pdb=" N PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 112.00 105.77 6.23 1.40e+00 5.10e-01 1.98e+01 angle pdb=" N PRO E 469 " pdb=" CA PRO E 469 " pdb=" CB PRO E 469 " ideal model delta sigma weight residual 103.25 99.10 4.15 1.05e+00 9.07e-01 1.56e+01 ... (remaining 42749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 17786 23.11 - 46.22: 1465 46.22 - 69.33: 238 69.33 - 92.45: 54 92.45 - 115.56: 41 Dihedral angle restraints: 19584 sinusoidal: 8543 harmonic: 11041 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 -177.55 -89.45 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 140.48 -47.48 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" C THR A 676 " pdb=" N THR A 676 " pdb=" CA THR A 676 " pdb=" CB THR A 676 " ideal model delta harmonic sigma weight residual -122.00 -134.84 12.84 0 2.50e+00 1.60e-01 2.64e+01 ... (remaining 19581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4763 0.110 - 0.219: 210 0.219 - 0.329: 10 0.329 - 0.439: 1 0.439 - 0.549: 2 Chirality restraints: 4986 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.88e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.36e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.83e+01 ... (remaining 4983 not shown) Planarity restraints: 5493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 468 " -0.127 5.00e-02 4.00e+02 1.73e-01 4.77e+01 pdb=" N PRO E 469 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO E 469 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO E 469 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO A 25 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " 0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO B 25 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.044 5.00e-02 4.00e+02 ... (remaining 5490 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 526 2.65 - 3.21: 27999 3.21 - 3.78: 45563 3.78 - 4.34: 62496 4.34 - 4.90: 102821 Nonbonded interactions: 239405 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.088 2.440 nonbonded pdb=" O GLU E 24 " pdb=" OG1 THR E 28 " model vdw 2.157 2.440 nonbonded pdb=" O ASP C 80 " pdb=" OH TYR C 265 " model vdw 2.166 2.440 nonbonded pdb=" NH1 ARG C 457 " pdb=" OG SER C 459 " model vdw 2.169 2.520 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.207 2.440 ... (remaining 239400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 257 or resid 262 through 1147 or resid 1301 thr \ ough 1304)) selection = (chain 'B' and (resid 14 through 141 or resid 154 through 176 or resid 188 throu \ gh 1147 or resid 1301 through 1304)) selection = (chain 'C' and (resid 14 through 141 or resid 154 through 176 or resid 188 throu \ gh 257 or resid 262 through 1147 or resid 1301 through 1304)) } ncs_group { reference = chain 'D' 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' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 19.090 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 86.060 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.410 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:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.007 0.176 31417 Z= 0.429 Angle : 0.767 18.862 42754 Z= 0.396 Chirality : 0.055 0.549 4986 Planarity : 0.006 0.173 5449 Dihedral : 17.321 115.557 12341 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.76 % Rotamer: Outliers : 1.45 % Allowed : 23.64 % Favored : 74.92 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.51 % 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: -0.67 (0.13), residues: 3738 helix: 0.31 (0.17), residues: 871 sheet: 0.44 (0.21), residues: 655 loop : -1.06 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 633 HIS 0.011 0.003 HIS A 245 PHE 0.042 0.003 PHE C 168 TYR 0.033 0.002 TYR C 170 ARG 0.009 0.001 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 83 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 ASN cc_start: 0.3584 (OUTLIER) cc_final: 0.2288 (p0) REVERT: E 270 MET cc_start: 0.2095 (mmm) cc_final: -0.0061 (ppp) REVERT: E 323 MET cc_start: 0.0742 (tmt) cc_final: 0.0333 (tmt) REVERT: E 360 MET cc_start: 0.5443 (ptt) cc_final: 0.4899 (mmt) REVERT: E 366 MET cc_start: 0.1316 (mmm) cc_final: 0.0049 (tpt) REVERT: E 462 MET cc_start: 0.7391 (mpm) cc_final: 0.6424 (ppp) outliers start: 48 outliers final: 39 residues processed: 129 average time/residue: 1.0634 time to fit residues: 172.9783 Evaluate side-chains 113 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 73 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 83 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 40.0000 chunk 285 optimal weight: 0.0970 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 179 optimal weight: 0.1980 chunk 219 optimal weight: 0.9980 chunk 342 optimal weight: 6.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 314 GLN A 343 ASN A 414 GLN A 422 ASN A 437 ASN A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN A 957 GLN A1142 GLN B 14 GLN B 173 GLN B 218 GLN B 245 HIS B 317 ASN B 354 ASN B 360 ASN B 394 ASN B 422 ASN B 493 GLN B 544 ASN B 628 GLN B 658 ASN B 901 GLN B 955 ASN B1002 GLN B1142 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 207 HIS C 314 GLN C 321 GLN C 422 ASN C 450 ASN C 519 HIS C 613 GLN C 658 ASN C 675 GLN C 901 GLN C1002 GLN E 43 GLN E 59 ASN E 64 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN E 330 ASN E 345 HIS E 493 HIS E 524 GLN E 586 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 31417 Z= 0.155 Angle : 0.564 9.291 42754 Z= 0.282 Chirality : 0.045 0.323 4986 Planarity : 0.004 0.089 5449 Dihedral : 11.556 106.287 5479 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.65 % Allowed : 22.76 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.11 (0.14), residues: 3738 helix: 1.36 (0.18), residues: 903 sheet: 0.68 (0.21), residues: 645 loop : -0.96 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 633 HIS 0.005 0.001 HIS E 374 PHE 0.022 0.001 PHE C 168 TYR 0.018 0.001 TYR B1067 ARG 0.007 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 74 time to evaluate : 3.490 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: E 54 ASN cc_start: 0.3410 (OUTLIER) cc_final: 0.2788 (m-40) REVERT: E 366 MET cc_start: 0.1028 (mmm) cc_final: 0.0147 (mmm) REVERT: E 579 MET cc_start: 0.2349 (mmt) cc_final: 0.1882 (mmt) outliers start: 88 outliers final: 27 residues processed: 156 average time/residue: 1.0305 time to fit residues: 204.2567 Evaluate side-chains 101 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 54 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 284 optimal weight: 0.7980 chunk 233 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 342 optimal weight: 40.0000 chunk 370 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 340 optimal weight: 40.0000 chunk 116 optimal weight: 9.9990 chunk 275 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 394 ASN B 544 ASN B 992 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 804 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 31417 Z= 0.399 Angle : 0.626 10.952 42754 Z= 0.311 Chirality : 0.047 0.320 4986 Planarity : 0.004 0.061 5449 Dihedral : 10.087 100.170 5446 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.70 % Allowed : 21.47 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.18 (0.14), residues: 3738 helix: 1.52 (0.18), residues: 897 sheet: 0.34 (0.19), residues: 724 loop : -1.04 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 633 HIS 0.006 0.001 HIS E 378 PHE 0.021 0.002 PHE C 800 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 76 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.7152 (t80) REVERT: A 425 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.5405 (pp) REVERT: A 900 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8975 (mtp) REVERT: E 54 ASN cc_start: 0.3193 (OUTLIER) cc_final: 0.2700 (m-40) REVERT: E 190 MET cc_start: 0.3191 (pp-130) cc_final: 0.2794 (pp-130) REVERT: E 366 MET cc_start: 0.1020 (mmm) cc_final: -0.0552 (mmm) REVERT: E 455 MET cc_start: 0.7473 (ppp) cc_final: 0.7232 (ppp) REVERT: E 462 MET cc_start: 0.7893 (mpm) cc_final: 0.7681 (mpp) REVERT: E 474 MET cc_start: -0.0043 (OUTLIER) cc_final: -0.0489 (tmm) REVERT: E 579 MET cc_start: 0.2047 (mmt) cc_final: 0.1624 (mmt) outliers start: 123 outliers final: 54 residues processed: 193 average time/residue: 0.9509 time to fit residues: 237.3106 Evaluate side-chains 133 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 74 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 8.9990 chunk 257 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 364 optimal weight: 20.0000 chunk 179 optimal weight: 0.9980 chunk 326 optimal weight: 50.0000 chunk 98 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 360 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A 965 GLN B 394 ASN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 31417 Z= 0.374 Angle : 0.607 11.330 42754 Z= 0.298 Chirality : 0.046 0.342 4986 Planarity : 0.004 0.055 5449 Dihedral : 9.376 97.469 5445 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.58 % Allowed : 22.13 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.21 (0.14), residues: 3738 helix: 1.60 (0.18), residues: 891 sheet: 0.29 (0.19), residues: 717 loop : -1.09 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 633 HIS 0.004 0.001 HIS E 493 PHE 0.019 0.001 PHE C 759 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 74 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.7154 (t80) REVERT: C 153 MET cc_start: 0.7434 (pmm) cc_final: 0.6460 (tpt) REVERT: E 54 ASN cc_start: 0.3628 (OUTLIER) cc_final: 0.3274 (m110) REVERT: E 190 MET cc_start: 0.3340 (pp-130) cc_final: 0.3006 (pp-130) REVERT: E 270 MET cc_start: 0.2198 (OUTLIER) cc_final: 0.1378 (tpp) REVERT: E 366 MET cc_start: 0.0871 (mmm) cc_final: -0.0613 (mmm) REVERT: E 474 MET cc_start: 0.0136 (OUTLIER) cc_final: -0.0337 (tmm) REVERT: E 579 MET cc_start: 0.2049 (mmt) cc_final: 0.1515 (mmt) outliers start: 119 outliers final: 66 residues processed: 189 average time/residue: 0.8763 time to fit residues: 221.6348 Evaluate side-chains 143 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 73 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 271 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 310 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 327 optimal weight: 40.0000 chunk 91 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31417 Z= 0.164 Angle : 0.541 9.608 42754 Z= 0.262 Chirality : 0.044 0.326 4986 Planarity : 0.003 0.051 5449 Dihedral : 8.586 95.310 5445 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.98 % Allowed : 22.67 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.06 (0.14), residues: 3738 helix: 1.71 (0.18), residues: 889 sheet: 0.37 (0.19), residues: 705 loop : -0.97 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 633 HIS 0.007 0.001 HIS B 245 PHE 0.017 0.001 PHE C 201 TYR 0.018 0.001 TYR A1067 ARG 0.002 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 75 time to evaluate : 3.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7191 (t80) REVERT: C 153 MET cc_start: 0.7531 (pmm) cc_final: 0.6908 (tpt) REVERT: C 168 PHE cc_start: 0.8392 (t80) cc_final: 0.8176 (t80) REVERT: E 54 ASN cc_start: 0.3502 (OUTLIER) cc_final: 0.3187 (m110) REVERT: E 116 ARG cc_start: 0.4288 (OUTLIER) cc_final: 0.4078 (ppt170) REVERT: E 190 MET cc_start: 0.3318 (pp-130) cc_final: 0.3057 (pp-130) REVERT: E 351 LEU cc_start: -0.0070 (OUTLIER) cc_final: -0.0511 (mt) REVERT: E 366 MET cc_start: 0.1091 (mmm) cc_final: -0.0446 (mmm) REVERT: E 455 MET cc_start: 0.7725 (ppp) cc_final: 0.7494 (ppp) REVERT: E 474 MET cc_start: -0.0153 (OUTLIER) cc_final: -0.0703 (tmm) REVERT: E 536 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.5367 (tp30) REVERT: E 579 MET cc_start: 0.1658 (mmt) cc_final: 0.1141 (mmt) outliers start: 99 outliers final: 50 residues processed: 168 average time/residue: 0.9238 time to fit residues: 200.6697 Evaluate side-chains 129 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 73 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 536 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 3.9990 chunk 328 optimal weight: 50.0000 chunk 72 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 364 optimal weight: 40.0000 chunk 302 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN C 907 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 31417 Z= 0.325 Angle : 0.583 9.738 42754 Z= 0.284 Chirality : 0.046 0.341 4986 Planarity : 0.004 0.048 5449 Dihedral : 8.430 94.007 5444 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.46 % Allowed : 22.28 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.09 (0.14), residues: 3738 helix: 1.71 (0.18), residues: 898 sheet: 0.34 (0.19), residues: 719 loop : -1.03 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 633 HIS 0.003 0.001 HIS E 493 PHE 0.018 0.001 PHE C 759 TYR 0.018 0.001 TYR A1067 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 75 time to evaluate : 4.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.5568 (OUTLIER) cc_final: 0.5338 (p0) REVERT: A 421 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.7223 (t80) REVERT: C 153 MET cc_start: 0.7659 (pmm) cc_final: 0.7145 (tpt) REVERT: C 515 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.7151 (p90) REVERT: E 54 ASN cc_start: 0.3407 (OUTLIER) cc_final: 0.3194 (m110) REVERT: E 116 ARG cc_start: 0.4278 (OUTLIER) cc_final: 0.4072 (ppt170) REVERT: E 160 ARG cc_start: 0.1701 (OUTLIER) cc_final: 0.0807 (tmt-80) REVERT: E 270 MET cc_start: 0.2870 (mpt) cc_final: -0.0761 (ptp) REVERT: E 351 LEU cc_start: -0.0028 (OUTLIER) cc_final: -0.0504 (mt) REVERT: E 366 MET cc_start: 0.1223 (mmm) cc_final: -0.0349 (mmm) REVERT: E 455 MET cc_start: 0.7774 (ppp) cc_final: 0.7519 (ppp) REVERT: E 474 MET cc_start: -0.0063 (OUTLIER) cc_final: -0.0668 (tmm) REVERT: E 579 MET cc_start: 0.1969 (mmt) cc_final: 0.1420 (mmt) outliers start: 115 outliers final: 74 residues processed: 183 average time/residue: 0.8587 time to fit residues: 206.5330 Evaluate side-chains 156 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 74 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 0.6980 chunk 266 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 363 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN C 613 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31417 Z= 0.241 Angle : 0.561 9.875 42754 Z= 0.272 Chirality : 0.045 0.340 4986 Planarity : 0.004 0.048 5449 Dihedral : 8.125 92.777 5444 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.92 % Allowed : 22.91 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.09 (0.14), residues: 3738 helix: 1.69 (0.18), residues: 907 sheet: 0.34 (0.19), residues: 724 loop : -1.03 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 633 HIS 0.003 0.001 HIS E 493 PHE 0.018 0.001 PHE C 168 TYR 0.026 0.001 TYR C 170 ARG 0.003 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 77 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7208 (t80) REVERT: B 153 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6402 (ttp) REVERT: B 277 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9303 (mt) REVERT: B 984 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7651 (tm) REVERT: C 153 MET cc_start: 0.7785 (pmm) cc_final: 0.7427 (tpt) REVERT: C 515 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7110 (p90) REVERT: E 116 ARG cc_start: 0.4261 (OUTLIER) cc_final: 0.4056 (ppt170) REVERT: E 160 ARG cc_start: 0.1738 (OUTLIER) cc_final: 0.1121 (tmt-80) REVERT: E 270 MET cc_start: 0.2878 (mpt) cc_final: -0.0793 (ptp) REVERT: E 366 MET cc_start: 0.1272 (mmm) cc_final: -0.0189 (mmm) REVERT: E 474 MET cc_start: -0.0024 (OUTLIER) cc_final: -0.0622 (tmm) REVERT: E 579 MET cc_start: 0.1956 (mmt) cc_final: 0.1415 (mmt) outliers start: 97 outliers final: 66 residues processed: 171 average time/residue: 0.9744 time to fit residues: 218.4472 Evaluate side-chains 149 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 75 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 217 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 285 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 360 ASN B 394 ASN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN C 613 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31417 Z= 0.282 Angle : 0.577 9.716 42754 Z= 0.279 Chirality : 0.045 0.344 4986 Planarity : 0.004 0.047 5449 Dihedral : 8.030 102.441 5442 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.43 % Allowed : 22.37 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3738 helix: 1.69 (0.18), residues: 907 sheet: 0.32 (0.19), residues: 724 loop : -1.03 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 633 HIS 0.004 0.001 HIS C 519 PHE 0.017 0.001 PHE A 392 TYR 0.018 0.001 TYR A1067 ARG 0.002 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 75 time to evaluate : 3.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.7225 (t80) REVERT: B 153 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6483 (ttp) REVERT: B 277 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9309 (mt) REVERT: B 984 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7738 (tm) REVERT: C 153 MET cc_start: 0.7874 (pmm) cc_final: 0.7567 (tpt) REVERT: C 515 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7150 (p90) REVERT: E 116 ARG cc_start: 0.4245 (OUTLIER) cc_final: 0.4023 (ppt170) REVERT: E 160 ARG cc_start: 0.1723 (OUTLIER) cc_final: 0.1138 (tmt-80) REVERT: E 270 MET cc_start: 0.2836 (mpt) cc_final: -0.0812 (ptp) REVERT: E 366 MET cc_start: 0.1327 (mmm) cc_final: -0.0165 (mmm) REVERT: E 474 MET cc_start: 0.0007 (OUTLIER) cc_final: -0.0643 (tmm) REVERT: E 516 TYR cc_start: 0.3869 (OUTLIER) cc_final: 0.3146 (m-80) REVERT: E 579 MET cc_start: 0.2066 (mmt) cc_final: 0.1525 (mmt) outliers start: 114 outliers final: 78 residues processed: 183 average time/residue: 0.8976 time to fit residues: 216.7555 Evaluate side-chains 161 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 74 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 516 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 9.9990 chunk 348 optimal weight: 6.9990 chunk 317 optimal weight: 0.0470 chunk 338 optimal weight: 40.0000 chunk 203 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 103 optimal weight: 0.0870 chunk 305 optimal weight: 4.9990 chunk 320 optimal weight: 50.0000 chunk 337 optimal weight: 9.9990 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31417 Z= 0.233 Angle : 0.574 9.685 42754 Z= 0.275 Chirality : 0.045 0.342 4986 Planarity : 0.004 0.048 5449 Dihedral : 7.814 100.436 5442 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.92 % Allowed : 22.94 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3738 helix: 1.71 (0.18), residues: 908 sheet: 0.34 (0.19), residues: 724 loop : -1.02 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 633 HIS 0.003 0.001 HIS E 493 PHE 0.035 0.001 PHE C 168 TYR 0.031 0.001 TYR C 170 ARG 0.002 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 77 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.7197 (t80) REVERT: B 153 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6448 (ttp) REVERT: B 984 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7709 (tm) REVERT: C 153 MET cc_start: 0.7886 (pmm) cc_final: 0.7605 (tpt) REVERT: C 515 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7165 (p90) REVERT: E 116 ARG cc_start: 0.4279 (OUTLIER) cc_final: 0.4054 (ppt170) REVERT: E 160 ARG cc_start: 0.1702 (OUTLIER) cc_final: 0.1142 (tmt-80) REVERT: E 270 MET cc_start: 0.2609 (mpt) cc_final: -0.0777 (ptp) REVERT: E 323 MET cc_start: 0.0635 (tmt) cc_final: -0.0153 (tmm) REVERT: E 366 MET cc_start: 0.1424 (mmm) cc_final: 0.0015 (mmm) REVERT: E 474 MET cc_start: -0.0032 (OUTLIER) cc_final: -0.0702 (tmm) REVERT: E 516 TYR cc_start: 0.3835 (OUTLIER) cc_final: 0.3144 (m-80) REVERT: E 579 MET cc_start: 0.1996 (mmt) cc_final: 0.1436 (mmt) outliers start: 97 outliers final: 78 residues processed: 170 average time/residue: 0.9220 time to fit residues: 204.8100 Evaluate side-chains 161 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 75 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 516 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 7.9990 chunk 358 optimal weight: 40.0000 chunk 218 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 375 optimal weight: 6.9990 chunk 345 optimal weight: 30.0000 chunk 299 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 183 optimal weight: 0.0980 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 360 ASN B 544 ASN B1002 GLN B1135 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 31417 Z= 0.503 Angle : 0.676 9.892 42754 Z= 0.332 Chirality : 0.048 0.369 4986 Planarity : 0.004 0.048 5449 Dihedral : 8.023 99.075 5442 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.04 % Allowed : 22.91 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.29 (0.14), residues: 3738 helix: 1.56 (0.18), residues: 909 sheet: 0.21 (0.19), residues: 716 loop : -1.16 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 633 HIS 0.006 0.001 HIS C 519 PHE 0.030 0.002 PHE C 759 TYR 0.017 0.001 TYR B1067 ARG 0.012 0.000 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 73 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7027 (t80) REVERT: B 153 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6772 (ttp) REVERT: B 188 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8167 (p0) REVERT: B 984 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7708 (tm) REVERT: C 153 MET cc_start: 0.7975 (pmm) cc_final: 0.7631 (tpt) REVERT: C 515 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.7144 (p90) REVERT: E 116 ARG cc_start: 0.4256 (OUTLIER) cc_final: 0.3982 (ppt170) REVERT: E 160 ARG cc_start: 0.1743 (OUTLIER) cc_final: 0.0874 (tmt-80) REVERT: E 270 MET cc_start: 0.2740 (mpt) cc_final: -0.0754 (ptp) REVERT: E 323 MET cc_start: 0.0886 (tmt) cc_final: -0.0021 (tmm) REVERT: E 366 MET cc_start: 0.1427 (mmm) cc_final: -0.0039 (mmm) REVERT: E 474 MET cc_start: 0.0141 (OUTLIER) cc_final: -0.0568 (tmm) REVERT: E 516 TYR cc_start: 0.3884 (OUTLIER) cc_final: 0.3118 (m-80) REVERT: E 579 MET cc_start: 0.2340 (mmt) cc_final: 0.1786 (mmt) outliers start: 101 outliers final: 74 residues processed: 171 average time/residue: 0.9669 time to fit residues: 218.9058 Evaluate side-chains 155 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 72 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 516 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 3.9990 chunk 318 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 299 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.103491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062894 restraints weight = 117371.144| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.65 r_work: 0.2745 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 31417 Z= 0.429 Angle : 0.788 59.165 42754 Z= 0.414 Chirality : 0.046 0.371 4986 Planarity : 0.004 0.066 5449 Dihedral : 8.030 99.119 5442 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 2.71 % Allowed : 23.25 % Favored : 74.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.51 % 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: -0.30 (0.14), residues: 3738 helix: 1.55 (0.18), residues: 909 sheet: 0.20 (0.19), residues: 716 loop : -1.16 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 633 HIS 0.005 0.001 HIS A 207 PHE 0.025 0.002 PHE C 759 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7762.94 seconds wall clock time: 143 minutes 44.49 seconds (8624.49 seconds total)