Starting phenix.real_space_refine on Sun Mar 24 04:18:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfx_34727/03_2024/8hfx_34727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfx_34727/03_2024/8hfx_34727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfx_34727/03_2024/8hfx_34727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfx_34727/03_2024/8hfx_34727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfx_34727/03_2024/8hfx_34727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfx_34727/03_2024/8hfx_34727.pdb" } resolution = 2.98 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= 0.061 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 9120 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 144 5.16 5 C 19655 2.51 5 N 5032 2.21 5 O 5975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1014": "OE1" <-> "OE2" Residue "B PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1115": "OD1" <-> "OD2" Residue "C PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "E PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30807 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8329 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 8 Chain: "B" Number of atoms: 8306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8306 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 59, 'TRANS': 998} Chain breaks: 7 Chain: "C" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8336 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 59, 'TRANS': 1002} Chain breaks: 7 Chain: "E" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4886 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 15.14, per 1000 atoms: 0.49 Number of scatterers: 30807 At special positions: 0 Unit cell: (141.95, 147.9, 254.15, 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 144 16.00 O 5975 8.00 N 5032 7.00 C 19655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.04 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.02 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.02 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.04 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 F 2 " - " BMA F 3 " " 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-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 231 " " NAG A1303 " - " ASN A 279 " " NAG A1304 " - " ASN A 706 " " NAG A1305 " - " ASN A1071 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A 340 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 120 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 160 " " NAG B1303 " - " ASN B 231 " " NAG B1304 " - " ASN B 279 " " NAG B1305 " - " ASN B 328 " " NAG B1306 " - " ASN B 340 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 613 " " NAG B1310 " - " ASN B 17 " " NAG B1311 " - " ASN B 120 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 120 " " NAG C1304 " - " ASN C 160 " " NAG C1305 " - " ASN C 231 " " NAG C1306 " - " ASN C 328 " " NAG C1307 " - " ASN C 340 " " NAG C1308 " - " ASN C 613 " " NAG D 1 " - " ASN E 54 " " NAG E 701 " - " ASN E 432 " " NAG E 702 " - " ASN E 299 " " NAG E 703 " - " ASN E 91 " " NAG F 1 " - " ASN E 546 " " NAG G 1 " - " ASN A 328 " " NAG H 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A1131 " " NAG L 1 " - " ASN B 714 " " NAG M 1 " - " ASN B 798 " " NAG N 1 " - " ASN B1095 " " NAG O 1 " - " ASN B1131 " " NAG P 1 " - " ASN C 279 " " NAG Q 1 " - " ASN C 706 " " NAG R 1 " - " ASN C 714 " " NAG S 1 " - " ASN C 798 " " NAG T 1 " - " ASN C1071 " " NAG U 1 " - " ASN C1095 " " NAG V 1 " - " ASN C1131 " Time building additional restraints: 11.97 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 704 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 374 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 378 " 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7118 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 42 sheets defined 30.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.017A pdb=" N TYR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.410A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.568A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.637A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.575A pdb=" N ASN A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 852 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.527A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.739A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 3.786A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.442A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.600A pdb=" N ASN B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.401A pdb=" N ARG B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.677A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 756 through 780 removed outlier: 3.633A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 846 through 852 Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.711A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 883 through 887' Processing helix chain 'B' and resid 894 through 906 removed outlier: 3.516A pdb=" N ARG B 902 " --> pdb=" O GLN B 898 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.697A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.699A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.861A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.700A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.455A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.605A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.958A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 419 removed outlier: 3.685A pdb=" N ASP C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.586A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.505A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.547A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.795A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 907 removed outlier: 3.639A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.324A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 916 " --> pdb=" O VAL C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.652A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER C 936 " --> pdb=" O GLN C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.687A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.145A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 4.360A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 54 removed outlier: 3.581A pdb=" N ALA E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 39 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 82 removed outlier: 3.527A pdb=" N LYS E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 102 removed outlier: 3.529A pdb=" N LEU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 130 removed outlier: 4.038A pdb=" N ARG E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR E 126 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR E 130 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.947A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 removed outlier: 4.594A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 176 " --> pdb=" O VAL E 172 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.826A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 4.253A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 252 removed outlier: 4.258A pdb=" N LYS E 224 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 227 " --> pdb=" O MET E 223 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR E 229 " --> pdb=" O ASP E 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE E 230 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.023A pdb=" N ASP E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 268 removed outlier: 3.688A pdb=" N GLY E 268 " --> pdb=" O HIS E 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 265 through 268' Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'E' and resid 294 through 299 removed outlier: 3.581A pdb=" N ASN E 299 " --> pdb=" O GLU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 316 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 365 through 386 removed outlier: 3.845A pdb=" N LEU E 370 " --> pdb=" O MET E 366 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 388 No H-bonds generated for 'chain 'E' and resid 387 through 388' Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.724A pdb=" N ARG E 393 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.659A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.742A pdb=" N ALA E 420 " --> pdb=" O HIS E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 449 removed outlier: 3.574A pdb=" N ILE E 436 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE E 446 " --> pdb=" O GLN E 442 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR E 449 " --> pdb=" O THR E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 removed outlier: 3.672A pdb=" N TRP E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS E 465 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 466 " --> pdb=" O MET E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 473 removed outlier: 3.752A pdb=" N GLN E 472 " --> pdb=" O PRO E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 485 removed outlier: 3.611A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 484 " --> pdb=" O MET E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 removed outlier: 3.677A pdb=" N GLU E 508 " --> pdb=" O PHE E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 533 removed outlier: 4.035A pdb=" N ILE E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS E 530 " --> pdb=" O HIS E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.553A pdb=" N GLN E 556 " --> pdb=" O GLN E 552 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET E 557 " --> pdb=" O ARG E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 4.347A pdb=" N ALA E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 574 " --> pdb=" O LEU E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 588 removed outlier: 4.450A pdb=" N ASN E 586 " --> pdb=" O LYS E 582 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR E 587 " --> pdb=" O PRO E 583 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 582 through 588' Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.689A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN E 599 " --> pdb=" O LEU E 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.544A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 200 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 221 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.003A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.478A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 119 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 124 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 167 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 316 removed outlier: 3.565A pdb=" N TYR A 310 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 325 removed outlier: 3.500A pdb=" N VAL A 573 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 584 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.887A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.638A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 377 removed outlier: 3.681A pdb=" N ALA A 432 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 657 removed outlier: 5.207A pdb=" N THR A 693 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A 655 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.762A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.669A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB5, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB6, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.408A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 260 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N HIS B 202 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N LEU B 220 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.053A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.007A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 167 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 128 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 308 through 316 removed outlier: 7.153A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.352A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC4, first strand: chain 'B' and resid 535 through 540 removed outlier: 4.150A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.931A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 698 through 701 Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.962A pdb=" N GLN B1068 " --> pdb=" O THR B 713 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE B 715 " --> pdb=" O PRO B1066 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 717 " --> pdb=" O TYR B1064 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B1064 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 719 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B1062 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 721 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B1060 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 723 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL B1058 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY B1056 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.962A pdb=" N GLN B1068 " --> pdb=" O THR B 713 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE B 715 " --> pdb=" O PRO B1066 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 717 " --> pdb=" O TYR B1064 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B1064 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 719 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B1062 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 721 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B1060 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 723 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL B1058 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY B1056 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.599A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.652A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS C 202 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ALA C 219 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.749A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.186A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN C 119 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 308 through 316 removed outlier: 7.201A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.532A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AD8, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AD9, first strand: chain 'C' and resid 536 through 540 removed outlier: 5.811A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.199A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.718A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.718A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AE5, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AE6, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.290A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 1164 hydrogen bonds defined for protein. 3228 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: 12.34 Time building geometry restraints manager: 12.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7524 1.33 - 1.46: 8040 1.46 - 1.58: 15777 1.58 - 1.71: 0 1.71 - 1.83: 193 Bond restraints: 31534 Sorted by residual: bond pdb=" N HIS E 322 " pdb=" CA HIS E 322 " ideal model delta sigma weight residual 1.454 1.499 -0.045 1.21e-02 6.83e+03 1.38e+01 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CA SER B 688 " pdb=" CB SER B 688 " ideal model delta sigma weight residual 1.534 1.476 0.058 1.76e-02 3.23e+03 1.07e+01 bond pdb=" N MET E 323 " pdb=" CA MET E 323 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.17e-02 7.31e+03 1.01e+01 ... (remaining 31529 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.72: 706 105.72 - 112.84: 16840 112.84 - 119.95: 10510 119.95 - 127.06: 14492 127.06 - 134.17: 337 Bond angle restraints: 42885 Sorted by residual: angle pdb=" N GLU A 337 " pdb=" CA GLU A 337 " pdb=" C GLU A 337 " ideal model delta sigma weight residual 112.93 101.25 11.68 1.33e+00 5.65e-01 7.71e+01 angle pdb=" C PRO A 334 " pdb=" CA PRO A 334 " pdb=" CB PRO A 334 " ideal model delta sigma weight residual 112.89 102.17 10.72 1.31e+00 5.83e-01 6.70e+01 angle pdb=" N PHE A 335 " pdb=" CA PHE A 335 " pdb=" C PHE A 335 " ideal model delta sigma weight residual 110.36 102.28 8.08 1.55e+00 4.16e-01 2.72e+01 angle pdb=" CA PHE A 335 " pdb=" C PHE A 335 " pdb=" O PHE A 335 " ideal model delta sigma weight residual 121.82 115.95 5.87 1.21e+00 6.83e-01 2.35e+01 angle pdb=" CA PRO A 984 " pdb=" N PRO A 984 " pdb=" CD PRO A 984 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 ... (remaining 42880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 18342 23.47 - 46.93: 1063 46.93 - 70.40: 192 70.40 - 93.86: 40 93.86 - 117.33: 53 Dihedral angle restraints: 19690 sinusoidal: 8649 harmonic: 11041 Sorted by residual: dihedral pdb=" CB CYS C 735 " pdb=" SG CYS C 735 " pdb=" SG CYS C 757 " pdb=" CB CYS C 757 " ideal model delta sinusoidal sigma weight residual 93.00 171.13 -78.13 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS E 530 " pdb=" SG CYS E 530 " pdb=" SG CYS E 542 " pdb=" CB CYS E 542 " ideal model delta sinusoidal sigma weight residual -86.00 -142.76 56.76 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 134 " pdb=" CB CYS C 134 " ideal model delta sinusoidal sigma weight residual -86.00 -134.55 48.55 1 1.00e+01 1.00e-02 3.25e+01 ... (remaining 19687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4655 0.097 - 0.195: 318 0.195 - 0.292: 13 0.292 - 0.390: 2 0.390 - 0.487: 3 Chirality restraints: 4991 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.67e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.56e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.29e+01 ... (remaining 4988 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 983 " -0.078 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 984 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 541 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ASN B 541 " 0.069 2.00e-02 2.50e+03 pdb=" O ASN B 541 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY B 542 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 503 " -0.055 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO A 504 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " -0.045 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 745 2.69 - 3.25: 28918 3.25 - 3.80: 44512 3.80 - 4.35: 59226 4.35 - 4.90: 100415 Nonbonded interactions: 233816 Sorted by model distance: nonbonded pdb=" OD1 ASP C 53 " pdb=" N LEU C 54 " model vdw 2.143 2.520 nonbonded pdb=" OG1 THR B 122 " pdb=" OD1 ASN B 123 " model vdw 2.175 2.440 nonbonded pdb=" OH TYR C 89 " pdb=" OE1 GLU C 186 " model vdw 2.192 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.198 2.440 nonbonded pdb=" OD1 ASN E 91 " pdb=" OG1 THR E 93 " model vdw 2.204 2.440 ... (remaining 233811 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 254 or resid 259 through 1144 or resid 1301 thr \ ough 1308)) selection = (chain 'B' and (resid 14 through 523 or resid 525 through 1144 or resid 1301 thr \ ough 1308)) selection = (chain 'C' and (resid 14 through 254 or resid 259 through 523 or resid 525 throu \ gh 1144 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' 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' } 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: 9.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.020 Extract box with map and model: 20.590 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 82.660 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.330 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:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.005 0.073 31534 Z= 0.321 Angle : 0.740 11.679 42885 Z= 0.390 Chirality : 0.052 0.487 4991 Planarity : 0.006 0.114 5441 Dihedral : 16.115 117.327 12449 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.78 % Allowed : 7.97 % Favored : 91.24 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.50 % 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: -0.61 (0.13), residues: 3724 helix: 0.31 (0.16), residues: 977 sheet: 0.70 (0.20), residues: 657 loop : -1.14 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 630 HIS 0.012 0.002 HIS E 535 PHE 0.025 0.003 PHE C 903 TYR 0.025 0.002 TYR E 385 ARG 0.021 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 248 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASN cc_start: 0.8120 (t0) cc_final: 0.7754 (t0) REVERT: A 342 THR cc_start: 0.4377 (OUTLIER) cc_final: 0.4030 (p) REVERT: A 406 GLN cc_start: 0.5982 (mt0) cc_final: 0.5739 (mt0) REVERT: A 495 ARG cc_start: 0.6888 (mtt90) cc_final: 0.6279 (mpp80) REVERT: A 737 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7944 (ttp) REVERT: B 148 MET cc_start: 0.2020 (tpt) cc_final: 0.1515 (ptm) REVERT: B 344 PHE cc_start: 0.6118 (m-80) cc_final: 0.5396 (m-80) REVERT: B 357 ASN cc_start: 0.6482 (t0) cc_final: 0.6173 (t0) REVERT: C 66 HIS cc_start: 0.6805 (t70) cc_final: 0.6579 (t-170) REVERT: C 486 TYR cc_start: 0.6551 (m-80) cc_final: 0.5524 (m-80) REVERT: E 24 GLU cc_start: 0.4186 (pt0) cc_final: 0.3724 (mt-10) REVERT: E 128 TYR cc_start: 0.1588 (t80) cc_final: 0.1318 (t80) REVERT: E 225 ASP cc_start: 0.1948 (m-30) cc_final: 0.1650 (t70) REVERT: E 228 ASN cc_start: 0.6617 (p0) cc_final: 0.5648 (m-40) REVERT: E 247 LYS cc_start: 0.2159 (mmmt) cc_final: 0.1487 (tppt) REVERT: E 320 LEU cc_start: 0.0325 (mm) cc_final: -0.0154 (tp) REVERT: E 351 LEU cc_start: 0.3659 (OUTLIER) cc_final: 0.3241 (tp) REVERT: E 408 MET cc_start: 0.2863 (pp-130) cc_final: 0.2314 (pmm) REVERT: E 417 TYR cc_start: 0.6136 (t80) cc_final: 0.5893 (t80) REVERT: E 508 GLU cc_start: 0.3697 (tt0) cc_final: 0.3081 (mt-10) outliers start: 26 outliers final: 9 residues processed: 266 average time/residue: 1.1148 time to fit residues: 365.3169 Evaluate side-chains 196 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 20.0000 chunk 284 optimal weight: 0.9990 chunk 158 optimal weight: 0.0060 chunk 97 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 152 optimal weight: 30.0000 chunk 294 optimal weight: 0.9990 chunk 114 optimal weight: 0.0770 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 9.9990 chunk 341 optimal weight: 30.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 191 ASN A 406 GLN A 445 ASN A 502 HIS ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN B 159 ASN B 357 ASN B 445 ASN B 561 GLN B 625 GLN B 759 GLN B 999 GLN C 311 GLN C 318 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31534 Z= 0.159 Angle : 0.560 10.686 42885 Z= 0.284 Chirality : 0.046 0.404 4991 Planarity : 0.004 0.050 5441 Dihedral : 11.872 102.692 5504 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.66 % Allowed : 9.84 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.02 (0.14), residues: 3724 helix: 1.21 (0.17), residues: 1019 sheet: 0.89 (0.19), residues: 696 loop : -0.97 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 630 HIS 0.010 0.001 HIS E 416 PHE 0.030 0.001 PHE B 163 TYR 0.021 0.001 TYR E 279 ARG 0.008 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 195 time to evaluate : 3.601 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.1633 (OUTLIER) cc_final: 0.0934 (pp-130) REVERT: A 331 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7635 (t0) REVERT: A 495 ARG cc_start: 0.6951 (mtt90) cc_final: 0.6340 (mpp80) REVERT: A 643 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7593 (ttm170) REVERT: B 148 MET cc_start: 0.1799 (tpt) cc_final: 0.1386 (ptm) REVERT: B 344 PHE cc_start: 0.6033 (m-80) cc_final: 0.5418 (m-80) REVERT: B 357 ASN cc_start: 0.6585 (OUTLIER) cc_final: 0.6330 (t0) REVERT: B 625 GLN cc_start: 0.5741 (OUTLIER) cc_final: 0.5180 (tp40) REVERT: C 66 HIS cc_start: 0.6573 (t70) cc_final: 0.6360 (t-170) REVERT: C 185 ARG cc_start: 0.7004 (mmt180) cc_final: 0.6793 (mmt-90) REVERT: C 486 TYR cc_start: 0.6313 (m-80) cc_final: 0.5417 (m-80) REVERT: C 748 ASN cc_start: 0.8007 (m-40) cc_final: 0.7684 (m-40) REVERT: E 196 TYR cc_start: 0.1873 (p90) cc_final: 0.0961 (m-10) REVERT: E 228 ASN cc_start: 0.6567 (p0) cc_final: 0.5727 (m-40) REVERT: E 247 LYS cc_start: 0.2278 (mmmt) cc_final: 0.1597 (tppt) REVERT: E 249 MET cc_start: 0.3195 (OUTLIER) cc_final: 0.2410 (tmm) REVERT: E 320 LEU cc_start: 0.0339 (mm) cc_final: -0.0088 (tp) REVERT: E 408 MET cc_start: 0.3049 (pp-130) cc_final: 0.2586 (pmm) REVERT: E 557 MET cc_start: 0.5425 (tmm) cc_final: 0.4060 (pmm) outliers start: 55 outliers final: 19 residues processed: 227 average time/residue: 1.0618 time to fit residues: 301.8854 Evaluate side-chains 188 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1139 GLN Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 332 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 284 optimal weight: 0.7980 chunk 232 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 369 optimal weight: 9.9990 chunk 304 optimal weight: 0.7980 chunk 339 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 445 ASN A 502 HIS ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31534 Z= 0.329 Angle : 0.610 10.732 42885 Z= 0.306 Chirality : 0.048 0.431 4991 Planarity : 0.004 0.047 5441 Dihedral : 9.661 96.966 5494 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.84 % Allowed : 11.38 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.10 (0.14), residues: 3724 helix: 1.24 (0.17), residues: 1020 sheet: 0.66 (0.19), residues: 714 loop : -1.07 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 883 HIS 0.006 0.001 HIS E 416 PHE 0.035 0.002 PHE B 903 TYR 0.021 0.002 TYR B1064 ARG 0.005 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 174 time to evaluate : 3.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.1700 (OUTLIER) cc_final: 0.0198 (pmm) REVERT: A 331 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7813 (t0) REVERT: A 490 ARG cc_start: 0.5359 (mmm-85) cc_final: 0.5047 (tmt170) REVERT: B 148 MET cc_start: 0.1660 (tpt) cc_final: 0.1281 (ptm) REVERT: B 344 PHE cc_start: 0.6375 (m-80) cc_final: 0.5930 (m-80) REVERT: B 970 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7708 (pt) REVERT: C 185 ARG cc_start: 0.7011 (mmt180) cc_final: 0.6802 (mmt-90) REVERT: C 371 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6689 (p90) REVERT: C 748 ASN cc_start: 0.8125 (m-40) cc_final: 0.7848 (m-40) REVERT: E 196 TYR cc_start: 0.1900 (p90) cc_final: 0.0871 (m-10) REVERT: E 247 LYS cc_start: 0.2413 (mmmt) cc_final: 0.1950 (tppt) REVERT: E 274 PHE cc_start: 0.4775 (t80) cc_final: 0.4563 (t80) REVERT: E 291 ILE cc_start: 0.3336 (OUTLIER) cc_final: 0.2914 (tp) REVERT: E 320 LEU cc_start: 0.0606 (mm) cc_final: 0.0013 (tp) REVERT: E 323 MET cc_start: 0.5720 (pp-130) cc_final: 0.5078 (ppp) REVERT: E 557 MET cc_start: 0.5561 (tmm) cc_final: 0.4098 (pmm) REVERT: E 571 GLU cc_start: 0.3272 (mt-10) cc_final: 0.2859 (pt0) outliers start: 61 outliers final: 25 residues processed: 210 average time/residue: 1.1314 time to fit residues: 293.5175 Evaluate side-chains 188 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 330 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 343 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 325 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN A 502 HIS A 610 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN B 759 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN E 35 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31534 Z= 0.201 Angle : 0.526 10.647 42885 Z= 0.263 Chirality : 0.045 0.340 4991 Planarity : 0.004 0.050 5441 Dihedral : 8.185 87.710 5493 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.02 % Allowed : 12.22 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.07 (0.14), residues: 3724 helix: 1.47 (0.17), residues: 1010 sheet: 0.76 (0.19), residues: 727 loop : -1.01 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 630 HIS 0.006 0.001 HIS E 416 PHE 0.017 0.001 PHE A1118 TYR 0.017 0.001 TYR C1064 ARG 0.009 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 172 time to evaluate : 3.781 Fit side-chains revert: symmetry clash REVERT: A 331 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7742 (m-40) REVERT: A 490 ARG cc_start: 0.5454 (mmm-85) cc_final: 0.5115 (tmt170) REVERT: A 495 ARG cc_start: 0.6918 (mtt90) cc_final: 0.6307 (mpp80) REVERT: A 737 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7910 (ttp) REVERT: B 148 MET cc_start: 0.1518 (tpt) cc_final: 0.1259 (ptm) REVERT: B 583 ASP cc_start: 0.7412 (m-30) cc_final: 0.7079 (m-30) REVERT: C 135 ASN cc_start: 0.5269 (OUTLIER) cc_final: 0.4956 (t0) REVERT: C 371 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6691 (p90) REVERT: C 405 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7561 (ptm160) REVERT: C 748 ASN cc_start: 0.8125 (m-40) cc_final: 0.7802 (m-40) REVERT: E 196 TYR cc_start: 0.2029 (p90) cc_final: 0.1095 (m-10) REVERT: E 247 LYS cc_start: 0.2239 (mmmt) cc_final: 0.1857 (tppt) REVERT: E 274 PHE cc_start: 0.4778 (t80) cc_final: 0.4577 (t80) REVERT: E 291 ILE cc_start: 0.3430 (OUTLIER) cc_final: 0.2980 (tp) REVERT: E 320 LEU cc_start: 0.0797 (mm) cc_final: 0.0239 (tp) REVERT: E 557 MET cc_start: 0.5574 (tmm) cc_final: 0.4165 (pmm) REVERT: E 571 GLU cc_start: 0.3304 (mt-10) cc_final: 0.2852 (pt0) outliers start: 67 outliers final: 29 residues processed: 215 average time/residue: 1.1285 time to fit residues: 300.9104 Evaluate side-chains 192 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 5.9990 chunk 206 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 310 optimal weight: 0.6980 chunk 251 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 185 optimal weight: 4.9990 chunk 326 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN A 502 HIS A 610 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN C 445 ASN C 898 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 31534 Z= 0.385 Angle : 0.613 11.795 42885 Z= 0.307 Chirality : 0.048 0.410 4991 Planarity : 0.004 0.046 5441 Dihedral : 8.295 90.109 5491 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.41 % Allowed : 13.09 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.17 (0.13), residues: 3724 helix: 1.24 (0.17), residues: 1024 sheet: 0.63 (0.19), residues: 715 loop : -1.16 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 883 HIS 0.009 0.001 HIS E 378 PHE 0.021 0.002 PHE A1118 TYR 0.023 0.002 TYR C 262 ARG 0.004 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 163 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7578 (mp) REVERT: A 165 TYR cc_start: 0.7218 (t80) cc_final: 0.6913 (t80) REVERT: A 331 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7753 (m-40) REVERT: B 148 MET cc_start: 0.1406 (tpt) cc_final: 0.1189 (ptm) REVERT: C 371 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6621 (p90) REVERT: C 405 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7539 (ptm160) REVERT: E 112 GLU cc_start: 0.4835 (OUTLIER) cc_final: 0.4443 (pt0) REVERT: E 202 TYR cc_start: 0.5087 (t80) cc_final: 0.4757 (m-80) REVERT: E 274 PHE cc_start: 0.4752 (t80) cc_final: 0.4527 (t80) REVERT: E 291 ILE cc_start: 0.3632 (OUTLIER) cc_final: 0.3244 (tp) REVERT: E 323 MET cc_start: 0.5293 (pp-130) cc_final: 0.4999 (ppp) REVERT: E 325 GLN cc_start: 0.5605 (mt0) cc_final: 0.5222 (mp10) REVERT: E 557 MET cc_start: 0.5662 (tmm) cc_final: 0.4301 (pmm) REVERT: E 571 GLU cc_start: 0.3303 (mt-10) cc_final: 0.2857 (pt0) outliers start: 80 outliers final: 41 residues processed: 216 average time/residue: 1.1335 time to fit residues: 301.7645 Evaluate side-chains 199 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 363 optimal weight: 9.9990 chunk 301 optimal weight: 0.0470 chunk 168 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 445 ASN A 502 HIS ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31534 Z= 0.294 Angle : 0.570 11.736 42885 Z= 0.285 Chirality : 0.046 0.444 4991 Planarity : 0.004 0.047 5441 Dihedral : 7.987 88.664 5491 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.44 % Allowed : 14.14 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.13 (0.14), residues: 3724 helix: 1.28 (0.17), residues: 1024 sheet: 0.65 (0.19), residues: 725 loop : -1.15 (0.13), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 630 HIS 0.008 0.001 HIS E 374 PHE 0.019 0.001 PHE A1118 TYR 0.019 0.001 TYR C 262 ARG 0.011 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 160 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7708 (m-40) REVERT: A 495 ARG cc_start: 0.6864 (mtt90) cc_final: 0.6267 (mpp80) REVERT: C 127 LYS cc_start: 0.7921 (ttpp) cc_final: 0.7531 (ttpp) REVERT: C 135 ASN cc_start: 0.5601 (OUTLIER) cc_final: 0.5276 (t0) REVERT: C 405 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7570 (ptm160) REVERT: E 112 GLU cc_start: 0.4955 (pp20) cc_final: 0.4609 (pt0) REVERT: E 274 PHE cc_start: 0.4780 (t80) cc_final: 0.4551 (t80) REVERT: E 325 GLN cc_start: 0.5530 (mt0) cc_final: 0.5254 (mp10) REVERT: E 557 MET cc_start: 0.5774 (tmm) cc_final: 0.4354 (pmm) REVERT: E 571 GLU cc_start: 0.3348 (mt-10) cc_final: 0.2863 (pt0) outliers start: 81 outliers final: 47 residues processed: 221 average time/residue: 1.1258 time to fit residues: 306.9472 Evaluate side-chains 202 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 152 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 chunk 205 optimal weight: 0.0980 chunk 306 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN A 502 HIS ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31534 Z= 0.184 Angle : 0.538 14.333 42885 Z= 0.268 Chirality : 0.045 0.394 4991 Planarity : 0.004 0.046 5441 Dihedral : 7.700 85.693 5491 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.29 % Allowed : 14.66 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.02 (0.14), residues: 3724 helix: 1.45 (0.17), residues: 1019 sheet: 0.73 (0.19), residues: 725 loop : -1.08 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 630 HIS 0.009 0.001 HIS E 374 PHE 0.026 0.001 PHE A 163 TYR 0.017 0.001 TYR C 262 ARG 0.008 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 162 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.1804 (OUTLIER) cc_final: 0.0314 (pmm) REVERT: A 331 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7688 (m-40) REVERT: A 495 ARG cc_start: 0.6865 (mtt90) cc_final: 0.6240 (mpp80) REVERT: C 127 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7518 (ttpp) REVERT: C 135 ASN cc_start: 0.5630 (OUTLIER) cc_final: 0.5334 (t0) REVERT: C 405 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7599 (ptm160) REVERT: E 112 GLU cc_start: 0.5025 (OUTLIER) cc_final: 0.4675 (pt0) REVERT: E 249 MET cc_start: 0.2920 (OUTLIER) cc_final: 0.2347 (tmm) REVERT: E 291 ILE cc_start: 0.3885 (OUTLIER) cc_final: 0.3496 (tp) REVERT: E 324 THR cc_start: 0.4740 (t) cc_final: 0.4248 (p) REVERT: E 325 GLN cc_start: 0.5367 (mt0) cc_final: 0.5037 (mp10) REVERT: E 557 MET cc_start: 0.5873 (tmm) cc_final: 0.4538 (pmm) REVERT: E 571 GLU cc_start: 0.3413 (mt-10) cc_final: 0.2971 (pt0) outliers start: 76 outliers final: 47 residues processed: 216 average time/residue: 1.0703 time to fit residues: 286.6489 Evaluate side-chains 211 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 157 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 330 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 20.0000 chunk 144 optimal weight: 0.7980 chunk 216 optimal weight: 9.9990 chunk 109 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN E 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31534 Z= 0.198 Angle : 0.538 15.225 42885 Z= 0.268 Chirality : 0.045 0.429 4991 Planarity : 0.004 0.047 5441 Dihedral : 7.478 83.794 5491 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.23 % Allowed : 14.96 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.07 (0.14), residues: 3724 helix: 1.49 (0.17), residues: 1025 sheet: 0.79 (0.19), residues: 724 loop : -1.06 (0.13), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 630 HIS 0.009 0.001 HIS E 374 PHE 0.017 0.001 PHE E 274 TYR 0.022 0.001 TYR A 165 ARG 0.005 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 167 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.1920 (OUTLIER) cc_final: 0.0504 (pmm) REVERT: A 331 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7667 (m-40) REVERT: A 495 ARG cc_start: 0.6848 (mtt90) cc_final: 0.6258 (mpp80) REVERT: B 583 ASP cc_start: 0.7476 (m-30) cc_final: 0.7163 (m-30) REVERT: C 135 ASN cc_start: 0.5898 (OUTLIER) cc_final: 0.5436 (t0) REVERT: C 405 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7602 (ptm160) REVERT: E 112 GLU cc_start: 0.5083 (OUTLIER) cc_final: 0.4761 (pt0) REVERT: E 291 ILE cc_start: 0.3943 (OUTLIER) cc_final: 0.3598 (tp) REVERT: E 324 THR cc_start: 0.4448 (t) cc_final: 0.3826 (p) REVERT: E 325 GLN cc_start: 0.5353 (mt0) cc_final: 0.5028 (mp10) REVERT: E 557 MET cc_start: 0.5858 (tmm) cc_final: 0.4610 (pmm) REVERT: E 571 GLU cc_start: 0.3526 (mt-10) cc_final: 0.3055 (pt0) outliers start: 74 outliers final: 48 residues processed: 219 average time/residue: 1.0943 time to fit residues: 297.7202 Evaluate side-chains 208 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 154 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 0.0470 chunk 347 optimal weight: 0.4980 chunk 316 optimal weight: 5.9990 chunk 337 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 319 optimal weight: 9.9990 chunk 336 optimal weight: 9.9990 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN C 66 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN C 932 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31534 Z= 0.232 Angle : 0.551 15.068 42885 Z= 0.275 Chirality : 0.045 0.384 4991 Planarity : 0.004 0.047 5441 Dihedral : 7.446 79.732 5489 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.02 % Allowed : 15.38 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.03 (0.14), residues: 3724 helix: 1.44 (0.17), residues: 1032 sheet: 0.74 (0.19), residues: 734 loop : -1.08 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 630 HIS 0.008 0.001 HIS E 374 PHE 0.035 0.001 PHE A 163 TYR 0.018 0.001 TYR C 262 ARG 0.005 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 157 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.1896 (OUTLIER) cc_final: 0.0528 (pmm) REVERT: A 331 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7635 (m-40) REVERT: C 135 ASN cc_start: 0.5814 (OUTLIER) cc_final: 0.5465 (t0) REVERT: C 405 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7576 (ptm160) REVERT: E 274 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.3387 (m-80) REVERT: E 291 ILE cc_start: 0.4087 (OUTLIER) cc_final: 0.3733 (tp) REVERT: E 324 THR cc_start: 0.4634 (t) cc_final: 0.3982 (p) REVERT: E 325 GLN cc_start: 0.5386 (mt0) cc_final: 0.5060 (mp10) REVERT: E 376 MET cc_start: 0.5915 (OUTLIER) cc_final: 0.5043 (ppp) REVERT: E 557 MET cc_start: 0.5882 (tmm) cc_final: 0.4628 (pmm) REVERT: E 571 GLU cc_start: 0.3520 (mt-10) cc_final: 0.3114 (pt0) outliers start: 67 outliers final: 48 residues processed: 207 average time/residue: 1.1760 time to fit residues: 299.7340 Evaluate side-chains 206 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 151 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 5.9990 chunk 357 optimal weight: 0.1980 chunk 217 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 374 optimal weight: 9.9990 chunk 344 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN C 66 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31534 Z= 0.264 Angle : 0.569 15.286 42885 Z= 0.283 Chirality : 0.046 0.413 4991 Planarity : 0.004 0.061 5441 Dihedral : 7.475 80.429 5489 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.78 % Allowed : 15.77 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.01 (0.14), residues: 3724 helix: 1.43 (0.17), residues: 1026 sheet: 0.68 (0.19), residues: 740 loop : -1.07 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 630 HIS 0.008 0.001 HIS E 374 PHE 0.018 0.001 PHE A1118 TYR 0.021 0.001 TYR A 165 ARG 0.016 0.000 ARG A 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 159 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.1754 (OUTLIER) cc_final: 0.0465 (pmm) REVERT: A 331 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7581 (m-40) REVERT: C 127 LYS cc_start: 0.8016 (ttpp) cc_final: 0.7619 (ttpp) REVERT: C 135 ASN cc_start: 0.5842 (OUTLIER) cc_final: 0.5493 (t0) REVERT: C 405 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7585 (ptm160) REVERT: E 274 PHE cc_start: 0.5576 (OUTLIER) cc_final: 0.3337 (m-80) REVERT: E 289 PRO cc_start: 0.5654 (Cg_exo) cc_final: 0.5367 (Cg_endo) REVERT: E 291 ILE cc_start: 0.3903 (OUTLIER) cc_final: 0.3540 (tp) REVERT: E 324 THR cc_start: 0.4581 (t) cc_final: 0.3940 (p) REVERT: E 325 GLN cc_start: 0.5450 (mt0) cc_final: 0.5096 (mp10) REVERT: E 557 MET cc_start: 0.5638 (tmm) cc_final: 0.4492 (pmm) REVERT: E 571 GLU cc_start: 0.3584 (mt-10) cc_final: 0.3172 (pt0) outliers start: 59 outliers final: 47 residues processed: 201 average time/residue: 1.2251 time to fit residues: 305.2842 Evaluate side-chains 208 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 155 time to evaluate : 3.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 848 CYS Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 932 GLN Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 274 PHE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 0.9990 chunk 317 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 306 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN C 66 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.156677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095026 restraints weight = 50546.427| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.39 r_work: 0.3102 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31534 Z= 0.235 Angle : 0.560 15.440 42885 Z= 0.278 Chirality : 0.045 0.424 4991 Planarity : 0.004 0.065 5441 Dihedral : 7.408 79.417 5489 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.78 % Allowed : 15.86 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.04 (0.14), residues: 3724 helix: 1.48 (0.17), residues: 1014 sheet: 0.73 (0.19), residues: 734 loop : -1.06 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 630 HIS 0.008 0.001 HIS E 374 PHE 0.035 0.001 PHE A 163 TYR 0.018 0.001 TYR C 262 ARG 0.015 0.000 ARG A 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8235.68 seconds wall clock time: 152 minutes 58.79 seconds (9178.79 seconds total)