Starting phenix.real_space_refine on Thu Mar 21 13:47:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt8_32771/03_2024/7wt8_32771.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt8_32771/03_2024/7wt8_32771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt8_32771/03_2024/7wt8_32771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt8_32771/03_2024/7wt8_32771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt8_32771/03_2024/7wt8_32771.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt8_32771/03_2024/7wt8_32771.pdb" } resolution = 3.6 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= -0.002 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 19238 2.51 5 N 4959 2.21 5 O 5910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1038": "OD1" <-> "OD2" Residue "A TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 983": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30240 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 900 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "J" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 900 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.99, per 1000 atoms: 0.50 Number of scatterers: 30240 At special positions: 0 Unit cell: (147.66, 147.66, 246.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 5910 8.00 N 4959 7.00 C 19238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.04 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " 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=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 163 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 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=2.04 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 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 356 " distance=2.03 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 520 " distance=2.04 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 733 " - pdb=" SG CYS C 755 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C1027 " - pdb=" SG CYS C1038 " distance=2.03 Simple disulfide: pdb=" SG CYS C1077 " - pdb=" SG CYS C1121 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 162 " " NAG A1304 " - " ASN A 340 " " NAG A1305 " - " ASN A 600 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 706 " " NAG A1309 " - " ASN A1071 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 162 " " NAG B1306 " - " ASN B 328 " " NAG B1307 " - " ASN B 600 " " NAG B1308 " - " ASN B 613 " " NAG B1309 " - " ASN B 654 " " NAG B1310 " - " ASN B 706 " " NAG B1311 " - " ASN B1071 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 162 " " NAG C1305 " - " ASN C 277 " " NAG C1306 " - " ASN C 338 " " NAG C1307 " - " ASN C 598 " " NAG C1308 " - " ASN C 611 " " NAG C1309 " - " ASN C 652 " " NAG C1310 " - " ASN C 704 " " NAG C1311 " - " ASN C1069 " " NAG E 1 " - " ASN A 279 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN A 714 " " NAG K 1 " - " ASN A 798 " " NAG L 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG N 1 " - " ASN B 340 " " NAG O 1 " - " ASN B 714 " " NAG P 1 " - " ASN B 798 " " NAG Q 1 " - " ASN B1095 " " NAG R 1 " - " ASN B1131 " " NAG S 1 " - " ASN C 326 " " NAG T 1 " - " ASN C 712 " " NAG U 1 " - " ASN C 796 " " NAG V 1 " - " ASN C1093 " " NAG W 1 " - " ASN C1129 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.15 Conformation dependent library (CDL) restraints added in 4.9 seconds 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 58 sheets defined 20.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.853A pdb=" N LEU A 365 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.942A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.682A pdb=" N ILE A 407 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.724A pdb=" N THR A 635 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 744 through 749 removed outlier: 3.573A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 744 through 749' Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 779 removed outlier: 3.738A pdb=" N GLU A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 771 " --> pdb=" O ILE A 767 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 824 removed outlier: 3.857A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 879 removed outlier: 3.710A pdb=" N ILE A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.597A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 936 " --> pdb=" O GLN A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.603A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (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 981 removed outlier: 3.747A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1027 removed outlier: 3.645A pdb=" N ALA A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A1003 " --> pdb=" O GLN A 999 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1024 " --> pdb=" O ASN A1020 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A1027 " --> pdb=" O ALA A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1147 removed outlier: 4.082A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1156 Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.800A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.405A pdb=" N ALA B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.611A pdb=" N LEU B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 388' Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.793A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 630 through 635 removed outlier: 4.127A pdb=" N TYR B 633 " --> pdb=" O TRP B 630 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR B 635 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 754 removed outlier: 3.564A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 4.134A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN B 776 " --> pdb=" O ASP B 772 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 777 " --> pdb=" O LYS B 773 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 780 " --> pdb=" O GLN B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.599A pdb=" N LEU B 818 " --> pdb=" O PRO B 814 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 removed outlier: 3.604A pdb=" N ALA B 876 " --> pdb=" O SER B 872 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 879 " --> pdb=" O LEU B 875 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 909 through 913 removed outlier: 4.086A pdb=" N VAL B 912 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 4.129A pdb=" N ILE B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.160A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 962 " --> pdb=" O THR B 958 " (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 974 through 980 removed outlier: 3.596A pdb=" N PHE B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER B 979 " --> pdb=" O ASN B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1024 removed outlier: 3.536A pdb=" N ASP B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B1004 " --> pdb=" O SER B1000 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B1017 " --> pdb=" O ALA B1013 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1155 removed outlier: 3.681A pdb=" N PHE B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B1155 " --> pdb=" O LYS B1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.900A pdb=" N PHE C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 364 removed outlier: 3.512A pdb=" N LEU C 363 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR C 364 " --> pdb=" O SER C 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 360 through 364' Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 611 through 613 No H-bonds generated for 'chain 'C' and resid 611 through 613' Processing helix chain 'C' and resid 614 through 620 removed outlier: 3.600A pdb=" N ALA C 618 " --> pdb=" O GLU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 738 removed outlier: 3.623A pdb=" N TYR C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 752 removed outlier: 3.664A pdb=" N LEU C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 749 " --> pdb=" O SER C 745 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 760 Processing helix chain 'C' and resid 764 through 777 removed outlier: 4.725A pdb=" N ASP C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 774 " --> pdb=" O ASP C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 861 through 876 removed outlier: 3.502A pdb=" N GLY C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 885 removed outlier: 3.520A pdb=" N GLY C 884 " --> pdb=" O TRP C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 900 removed outlier: 4.627A pdb=" N MET C 897 " --> pdb=" O PRO C 894 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA C 898 " --> pdb=" O MET C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 913 removed outlier: 3.585A pdb=" N LEU C 911 " --> pdb=" O GLN C 908 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR C 912 " --> pdb=" O ASN C 909 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 913 " --> pdb=" O VAL C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 934 removed outlier: 3.647A pdb=" N ILE C 929 " --> pdb=" O ALA C 925 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP C 931 " --> pdb=" O GLY C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 960 removed outlier: 3.561A pdb=" N VAL C 946 " --> pdb=" O LYS C 942 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 950 " --> pdb=" O VAL C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 971 through 979 removed outlier: 4.339A pdb=" N ILE C 975 " --> pdb=" O VAL C 971 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE C 976 " --> pdb=" O LEU C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 1027 removed outlier: 3.656A pdb=" N VAL C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C1011 " --> pdb=" O LEU C1007 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C1016 " --> pdb=" O GLU C1012 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C1025 " --> pdb=" O ALA C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1153 removed outlier: 3.511A pdb=" N GLU C1139 " --> pdb=" O PRO C1135 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE C1143 " --> pdb=" O GLU C1139 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU C1146 " --> pdb=" O SER C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.585A pdb=" N ASP D 82 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 83' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.645A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.280A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 63 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 264 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 262 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 67 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 260 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N SER A 202 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 54 removed outlier: 3.733A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.044A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.585A pdb=" N GLN A 134 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322 removed outlier: 7.021A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.633A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 394 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 355 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU A 513 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 399 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.553A pdb=" N TYR A 470 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 562 through 563 removed outlier: 6.760A pdb=" N PHE A 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 572 through 574 removed outlier: 7.034A pdb=" N VAL A 573 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 661 through 662 removed outlier: 3.552A pdb=" N ILE A 690 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 688 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 724 removed outlier: 7.183A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 724 Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB7, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AB8, first strand: chain 'A' and resid 1086 through 1087 Processing sheet with id=AB9, first strand: chain 'A' and resid 1091 through 1092 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.756A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 261 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.971A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.604A pdb=" N GLY B 107 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY B 103 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 130 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.151A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N SER B 159 " --> pdb=" O GLN B 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 308 through 313 removed outlier: 5.871A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 608 " --> pdb=" O SER B 593 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.662A pdb=" N GLY B 545 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 390 through 393 removed outlier: 5.203A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU B 513 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 399 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 397 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 390 through 393 removed outlier: 5.203A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU B 513 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP B 433 " --> pdb=" O ARG B 506 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 508 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.536A pdb=" N TYR B 470 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.138A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 672 " --> pdb=" O SER B 688 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 708 through 709 removed outlier: 3.555A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.536A pdb=" N ALA B1053 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 732 through 733 Processing sheet with id=AD6, first strand: chain 'B' and resid 1078 through 1079 removed outlier: 3.572A pdb=" N CYS B1079 " --> pdb=" O VAL B1130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.574A pdb=" N ASN C 61 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR C 264 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C 259 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N SER C 202 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.847A pdb=" N ASP C 282 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.744A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE C 133 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C 114 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS C 131 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER C 116 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS C 129 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 118 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 127 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C 120 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN C 125 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 126 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL C 168 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE C 128 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU C 166 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 130 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 349 through 351 removed outlier: 3.591A pdb=" N ALA C 392 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASN C 389 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 511 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AE4, first strand: chain 'C' and resid 533 through 534 Processing sheet with id=AE5, first strand: chain 'C' and resid 590 through 591 Processing sheet with id=AE6, first strand: chain 'C' and resid 649 through 655 removed outlier: 6.380A pdb=" N GLU C 649 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR C 691 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N VAL C 651 " --> pdb=" O THR C 691 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 706 through 710 Processing sheet with id=AE8, first strand: chain 'C' and resid 713 through 723 removed outlier: 3.510A pdb=" N SER C 716 " --> pdb=" O THR C1061 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 720 " --> pdb=" O PHE C1057 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C1060 " --> pdb=" O LEU C1044 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 713 through 723 removed outlier: 3.510A pdb=" N SER C 716 " --> pdb=" O THR C1061 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 720 " --> pdb=" O PHE C1057 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C1051 " --> pdb=" O GLY C1054 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 730 through 731 Processing sheet with id=AF2, first strand: chain 'C' and resid 1115 through 1117 removed outlier: 3.877A pdb=" N CYS C1077 " --> pdb=" O VAL C1128 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.600A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.704A pdb=" N THR D 74 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.670A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.632A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 10 through 11 Processing sheet with id=AF9, first strand: chain 'I' and resid 19 through 24 removed outlier: 3.700A pdb=" N ILE I 75 " --> pdb=" O VAL I 19 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.807A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AG3, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) 855 hydrogen bonds defined for protein. 2298 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: 12.13 Time building geometry restraints manager: 13.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 4882 1.30 - 1.43: 8455 1.43 - 1.57: 17425 1.57 - 1.70: 1 1.70 - 1.84: 171 Bond restraints: 30934 Sorted by residual: bond pdb=" C PRO C 892 " pdb=" O PRO C 892 " ideal model delta sigma weight residual 1.233 1.162 0.071 1.23e-02 6.61e+03 3.32e+01 bond pdb=" N VAL B1065 " pdb=" CA VAL B1065 " ideal model delta sigma weight residual 1.454 1.494 -0.039 7.70e-03 1.69e+04 2.58e+01 bond pdb=" CA SER A 813 " pdb=" CB SER A 813 " ideal model delta sigma weight residual 1.536 1.474 0.062 1.23e-02 6.61e+03 2.57e+01 bond pdb=" C PRO B 894 " pdb=" O PRO B 894 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.30e-02 5.92e+03 2.56e+01 bond pdb=" C PRO B1066 " pdb=" O PRO B1066 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.21e-02 6.83e+03 2.41e+01 ... (remaining 30929 not shown) Histogram of bond angle deviations from ideal: 95.10 - 103.51: 395 103.51 - 111.92: 14706 111.92 - 120.34: 13853 120.34 - 128.75: 12989 128.75 - 137.16: 145 Bond angle restraints: 42088 Sorted by residual: angle pdb=" CA PRO A 894 " pdb=" C PRO A 894 " pdb=" O PRO A 894 " ideal model delta sigma weight residual 121.27 111.60 9.67 1.05e+00 9.07e-01 8.48e+01 angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.27 95.10 8.17 9.00e-01 1.23e+00 8.24e+01 angle pdb=" N THR C 763 " pdb=" CA THR C 763 " pdb=" C THR C 763 " ideal model delta sigma weight residual 114.31 102.73 11.58 1.29e+00 6.01e-01 8.05e+01 angle pdb=" N PRO B 896 " pdb=" CA PRO B 896 " pdb=" C PRO B 896 " ideal model delta sigma weight residual 114.68 105.43 9.25 1.04e+00 9.25e-01 7.91e+01 angle pdb=" N GLN C 896 " pdb=" CA GLN C 896 " pdb=" C GLN C 896 " ideal model delta sigma weight residual 112.68 100.95 11.73 1.33e+00 5.65e-01 7.78e+01 ... (remaining 42083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 17850 22.90 - 45.80: 1211 45.80 - 68.71: 148 68.71 - 91.61: 34 91.61 - 114.51: 49 Dihedral angle restraints: 19292 sinusoidal: 8363 harmonic: 10929 Sorted by residual: dihedral pdb=" CA ASP B 142 " pdb=" C ASP B 142 " pdb=" N HIS B 143 " pdb=" CA HIS B 143 " ideal model delta harmonic sigma weight residual -180.00 -112.00 -68.00 0 5.00e+00 4.00e-02 1.85e+02 dihedral pdb=" CA ASP C 142 " pdb=" C ASP C 142 " pdb=" N HIS C 143 " pdb=" CA HIS C 143 " ideal model delta harmonic sigma weight residual -180.00 -118.19 -61.81 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA LEU C 215 " pdb=" C LEU C 215 " pdb=" N PRO C 216 " pdb=" CA PRO C 216 " ideal model delta harmonic sigma weight residual 180.00 131.67 48.33 0 5.00e+00 4.00e-02 9.34e+01 ... (remaining 19289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4477 0.100 - 0.199: 380 0.199 - 0.299: 54 0.299 - 0.399: 7 0.399 - 0.498: 4 Chirality restraints: 4922 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA PHE B 326 " pdb=" N PHE B 326 " pdb=" C PHE B 326 " pdb=" CB PHE B 326 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 798 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 4919 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 324 " 0.021 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C VAL B 324 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL B 324 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG B 325 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 886 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C GLY B 886 " 0.065 2.00e-02 2.50e+03 pdb=" O GLY B 886 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 887 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 333 " 0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO B 334 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 334 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 334 " 0.049 5.00e-02 4.00e+02 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2458 2.74 - 3.28: 28734 3.28 - 3.82: 47473 3.82 - 4.36: 54597 4.36 - 4.90: 94182 Nonbonded interactions: 227444 Sorted by model distance: nonbonded pdb=" O GLU C 656 " pdb=" OH TYR C 690 " model vdw 2.200 2.440 nonbonded pdb=" O GLY B 877 " pdb=" OG SER B 881 " model vdw 2.219 2.440 nonbonded pdb=" O TYR I 86 " pdb=" OG1 THR I 102 " model vdw 2.250 2.440 nonbonded pdb=" O GLU B 658 " pdb=" OH TYR B 692 " model vdw 2.252 2.440 nonbonded pdb=" OD1 ASP D 50 " pdb=" OH TYR D 91 " model vdw 2.265 2.440 ... (remaining 227439 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' selection = (chain 'B' and (resid 14 through 1159 or resid 1301 through 1309)) selection = (chain 'C' and (resid 14 through 1157 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.150 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 76.510 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.006 0.131 30934 Z= 0.393 Angle : 0.996 12.160 42088 Z= 0.606 Chirality : 0.063 0.498 4922 Planarity : 0.006 0.091 5360 Dihedral : 15.740 114.512 12137 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.62 % Favored : 92.03 % Rotamer: Outliers : 1.00 % Allowed : 1.40 % Favored : 97.60 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.11 % 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: -2.76 (0.13), residues: 3714 helix: -2.74 (0.15), residues: 624 sheet: -0.63 (0.20), residues: 689 loop : -2.04 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 883 HIS 0.007 0.001 HIS C1043 PHE 0.025 0.002 PHE C 893 TYR 0.018 0.002 TYR C 260 ARG 0.014 0.001 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 244 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 462 GLU cc_start: 0.7190 (pm20) cc_final: 0.6978 (pm20) REVERT: B 770 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7597 (tm-30) REVERT: C 217 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6238 (tm-30) REVERT: C 324 PHE cc_start: 0.4825 (OUTLIER) cc_final: 0.4284 (t80) REVERT: C 447 LEU cc_start: 0.6264 (mm) cc_final: 0.5912 (mm) REVERT: C 899 TYR cc_start: 0.7468 (m-10) cc_final: 0.7189 (m-10) REVERT: J 28 ILE cc_start: 0.3266 (mp) cc_final: 0.2865 (pt) outliers start: 33 outliers final: 13 residues processed: 275 average time/residue: 0.3952 time to fit residues: 179.8516 Evaluate side-chains 176 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 940 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 290 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 336 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN B 916 ASN C 143 HIS C 217 GLN C 750 GLN C 799 GLN C 890 GLN C 930 GLN I 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30934 Z= 0.213 Angle : 0.620 15.684 42088 Z= 0.313 Chirality : 0.046 0.350 4922 Planarity : 0.005 0.081 5360 Dihedral : 11.426 102.000 5390 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.79 % Favored : 93.11 % Rotamer: Outliers : 1.28 % Allowed : 8.55 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.06 % 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: -2.24 (0.13), residues: 3714 helix: -1.45 (0.18), residues: 659 sheet: -0.50 (0.20), residues: 706 loop : -1.89 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 36 HIS 0.004 0.001 HIS C 143 PHE 0.018 0.001 PHE B 397 TYR 0.020 0.001 TYR B 393 ARG 0.004 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7802 (mmtt) REVERT: C 42 VAL cc_start: 0.8789 (t) cc_final: 0.8551 (t) REVERT: C 324 PHE cc_start: 0.5322 (OUTLIER) cc_final: 0.5024 (m-80) REVERT: C 938 SER cc_start: 0.7470 (OUTLIER) cc_final: 0.6955 (t) REVERT: I 90 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5174 (pp30) REVERT: J 28 ILE cc_start: 0.3896 (mp) cc_final: 0.3562 (pt) outliers start: 42 outliers final: 28 residues processed: 213 average time/residue: 0.3890 time to fit residues: 138.7783 Evaluate side-chains 184 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 750 GLN Chi-restraints excluded: chain C residue 755 CYS Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 0.3980 chunk 280 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 337 optimal weight: 50.0000 chunk 364 optimal weight: 20.0000 chunk 300 optimal weight: 0.6980 chunk 334 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 270 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN C 908 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30934 Z= 0.276 Angle : 0.616 10.289 42088 Z= 0.311 Chirality : 0.046 0.361 4922 Planarity : 0.004 0.072 5360 Dihedral : 10.027 106.610 5379 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.98 % Rotamer: Outliers : 1.92 % Allowed : 11.99 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.13), residues: 3714 helix: -0.91 (0.19), residues: 662 sheet: -0.63 (0.19), residues: 727 loop : -1.89 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 149 HIS 0.004 0.001 HIS C 143 PHE 0.018 0.002 PHE C 901 TYR 0.021 0.001 TYR B 393 ARG 0.007 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 162 time to evaluate : 3.603 Fit side-chains revert: symmetry clash REVERT: A 87 ASN cc_start: 0.7509 (OUTLIER) cc_final: 0.6028 (p0) REVERT: A 115 GLN cc_start: 0.8257 (tp40) cc_final: 0.8035 (mm-40) REVERT: A 811 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7788 (mmtt) REVERT: B 462 GLU cc_start: 0.7439 (pm20) cc_final: 0.7131 (pm20) REVERT: C 42 VAL cc_start: 0.8830 (t) cc_final: 0.8609 (t) REVERT: H 6 GLU cc_start: 0.1290 (OUTLIER) cc_final: 0.0958 (tp30) REVERT: J 28 ILE cc_start: 0.4005 (mp) cc_final: 0.3604 (pt) outliers start: 63 outliers final: 47 residues processed: 218 average time/residue: 0.3767 time to fit residues: 138.9313 Evaluate side-chains 199 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 890 GLN Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain I residue 93 ASN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 79 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 30.0000 chunk 253 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 37 optimal weight: 30.0000 chunk 161 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 338 optimal weight: 20.0000 chunk 358 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 GLN C 930 GLN C 997 GLN D 30 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30934 Z= 0.256 Angle : 0.593 9.528 42088 Z= 0.299 Chirality : 0.046 0.362 4922 Planarity : 0.004 0.069 5360 Dihedral : 9.433 109.115 5376 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.65 % Favored : 92.25 % Rotamer: Outliers : 2.56 % Allowed : 13.55 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3714 helix: -0.71 (0.20), residues: 668 sheet: -0.66 (0.19), residues: 736 loop : -1.88 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 149 HIS 0.006 0.001 HIS B 951 PHE 0.017 0.001 PHE B1118 TYR 0.020 0.001 TYR B 393 ARG 0.005 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 164 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 899 MET cc_start: 0.9187 (tpt) cc_final: 0.8900 (tpt) REVERT: C 226 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8261 (m) REVERT: C 271 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6940 (tt) REVERT: H 6 GLU cc_start: 0.1413 (OUTLIER) cc_final: 0.0973 (tp30) REVERT: J 28 ILE cc_start: 0.4126 (mp) cc_final: 0.3673 (pt) outliers start: 84 outliers final: 61 residues processed: 237 average time/residue: 0.3695 time to fit residues: 149.3063 Evaluate side-chains 214 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 150 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 755 CYS Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 813 ILE Chi-restraints excluded: chain C residue 890 GLN Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 306 optimal weight: 0.0870 chunk 247 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 321 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30934 Z= 0.185 Angle : 0.563 9.195 42088 Z= 0.283 Chirality : 0.045 0.341 4922 Planarity : 0.004 0.064 5360 Dihedral : 8.875 110.061 5375 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.95 % Favored : 92.95 % Rotamer: Outliers : 2.53 % Allowed : 14.76 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.14), residues: 3714 helix: -0.37 (0.20), residues: 662 sheet: -0.52 (0.19), residues: 737 loop : -1.85 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 149 HIS 0.003 0.001 HIS C 143 PHE 0.016 0.001 PHE A 79 TYR 0.018 0.001 TYR C 167 ARG 0.006 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 169 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.5893 (p0) REVERT: A 300 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8019 (tt) REVERT: A 811 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7439 (ttpt) REVERT: A 899 MET cc_start: 0.9234 (tpt) cc_final: 0.8922 (tpt) REVERT: C 42 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8423 (t) REVERT: C 226 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8345 (m) REVERT: C 271 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6993 (tt) REVERT: H 6 GLU cc_start: 0.1433 (OUTLIER) cc_final: 0.0966 (tp30) REVERT: J 28 ILE cc_start: 0.4283 (mp) cc_final: 0.3758 (pt) REVERT: J 79 TYR cc_start: 0.4777 (OUTLIER) cc_final: 0.4502 (m-80) outliers start: 83 outliers final: 55 residues processed: 236 average time/residue: 0.3674 time to fit residues: 148.2744 Evaluate side-chains 214 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 152 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 79 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 120 optimal weight: 20.0000 chunk 322 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 358 optimal weight: 9.9990 chunk 297 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN A 898 GLN A 911 ASN A 952 ASN A1002 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 559 GLN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30934 Z= 0.385 Angle : 0.679 9.760 42088 Z= 0.344 Chirality : 0.049 0.413 4922 Planarity : 0.005 0.064 5360 Dihedral : 8.869 115.716 5372 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.05 % Favored : 90.85 % Rotamer: Outliers : 3.44 % Allowed : 15.62 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 3714 helix: -0.67 (0.20), residues: 668 sheet: -0.86 (0.19), residues: 750 loop : -1.99 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 149 HIS 0.005 0.001 HIS C1096 PHE 0.023 0.002 PHE A 55 TYR 0.024 0.002 TYR B 393 ARG 0.007 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 157 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7867 (OUTLIER) cc_final: 0.7640 (t60) REVERT: A 87 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.6559 (p0) REVERT: A 238 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: A 899 MET cc_start: 0.9147 (tpt) cc_final: 0.8816 (tpt) REVERT: B 350 TRP cc_start: 0.8804 (OUTLIER) cc_final: 0.8437 (p-90) REVERT: B 960 VAL cc_start: 0.9558 (OUTLIER) cc_final: 0.9251 (t) REVERT: C 150 MET cc_start: 0.4032 (tmm) cc_final: 0.3684 (tmm) REVERT: C 226 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8239 (m) REVERT: C 271 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7315 (mp) REVERT: C 868 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8426 (m-10) REVERT: H 6 GLU cc_start: 0.1605 (OUTLIER) cc_final: 0.1157 (tp30) REVERT: J 28 ILE cc_start: 0.4266 (mp) cc_final: 0.3782 (pt) outliers start: 113 outliers final: 74 residues processed: 259 average time/residue: 0.3561 time to fit residues: 158.5872 Evaluate side-chains 228 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 145 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 813 ILE Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 907 THR Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 50.0000 chunk 40 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 262 optimal weight: 0.0000 chunk 203 optimal weight: 0.7980 chunk 302 optimal weight: 0.0970 chunk 200 optimal weight: 0.4980 chunk 357 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 218 optimal weight: 40.0000 chunk 165 optimal weight: 0.5980 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 559 GLN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN D 93 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30934 Z= 0.144 Angle : 0.565 9.149 42088 Z= 0.283 Chirality : 0.045 0.336 4922 Planarity : 0.004 0.060 5360 Dihedral : 8.074 111.893 5372 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.17 % Favored : 93.70 % Rotamer: Outliers : 2.19 % Allowed : 17.44 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3714 helix: -0.17 (0.20), residues: 670 sheet: -0.55 (0.19), residues: 750 loop : -1.84 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 348 HIS 0.004 0.001 HIS C 143 PHE 0.023 0.001 PHE C 55 TYR 0.017 0.001 TYR C 418 ARG 0.005 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 163 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7663 (OUTLIER) cc_final: 0.7427 (t60) REVERT: A 87 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.6032 (p0) REVERT: A 219 PHE cc_start: 0.6462 (m-80) cc_final: 0.6188 (m-80) REVERT: A 300 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7988 (tt) REVERT: A 811 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7421 (tttt) REVERT: A 899 MET cc_start: 0.9248 (tpt) cc_final: 0.8948 (tpt) REVERT: B 271 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8492 (t) REVERT: B 350 TRP cc_start: 0.8613 (OUTLIER) cc_final: 0.8201 (p-90) REVERT: C 42 VAL cc_start: 0.8688 (t) cc_final: 0.8397 (t) REVERT: C 150 MET cc_start: 0.4135 (tmm) cc_final: 0.3748 (tmm) REVERT: H 6 GLU cc_start: 0.1474 (OUTLIER) cc_final: 0.1073 (tp30) REVERT: J 28 ILE cc_start: 0.4061 (mp) cc_final: 0.3542 (pt) outliers start: 72 outliers final: 49 residues processed: 222 average time/residue: 0.3782 time to fit residues: 143.0876 Evaluate side-chains 206 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 151 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 221 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 213 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 281 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 GLN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30934 Z= 0.163 Angle : 0.557 9.263 42088 Z= 0.278 Chirality : 0.045 0.340 4922 Planarity : 0.004 0.073 5360 Dihedral : 7.747 113.718 5370 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.65 % Rotamer: Outliers : 2.25 % Allowed : 17.75 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3714 helix: -0.01 (0.21), residues: 669 sheet: -0.46 (0.19), residues: 753 loop : -1.80 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 149 HIS 0.003 0.001 HIS C 143 PHE 0.018 0.001 PHE C 55 TYR 0.016 0.001 TYR B 393 ARG 0.005 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 160 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7674 (OUTLIER) cc_final: 0.7468 (t60) REVERT: A 87 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.5976 (p0) REVERT: A 300 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.8014 (tt) REVERT: B 271 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8526 (t) REVERT: B 350 TRP cc_start: 0.8628 (OUTLIER) cc_final: 0.8223 (p-90) REVERT: C 150 MET cc_start: 0.4005 (tmm) cc_final: 0.3660 (tmm) REVERT: H 6 GLU cc_start: 0.1379 (OUTLIER) cc_final: 0.1060 (tp30) REVERT: I 92 ASP cc_start: 0.5892 (t0) cc_final: 0.5614 (t0) REVERT: J 28 ILE cc_start: 0.4061 (mp) cc_final: 0.3543 (pt) outliers start: 74 outliers final: 58 residues processed: 221 average time/residue: 0.3689 time to fit residues: 138.4002 Evaluate side-chains 214 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 150 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 325 optimal weight: 5.9990 chunk 342 optimal weight: 6.9990 chunk 312 optimal weight: 0.6980 chunk 333 optimal weight: 9.9990 chunk 200 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 301 optimal weight: 0.9990 chunk 315 optimal weight: 4.9990 chunk 332 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 GLN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30934 Z= 0.170 Angle : 0.557 9.508 42088 Z= 0.277 Chirality : 0.045 0.339 4922 Planarity : 0.004 0.066 5360 Dihedral : 7.528 112.787 5370 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.41 % Favored : 93.46 % Rotamer: Outliers : 2.25 % Allowed : 18.11 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3714 helix: 0.11 (0.21), residues: 669 sheet: -0.49 (0.19), residues: 760 loop : -1.78 (0.13), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 149 HIS 0.004 0.001 HIS B 951 PHE 0.018 0.001 PHE C 55 TYR 0.017 0.001 TYR C 167 ARG 0.013 0.000 ARG B1104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 162 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7672 (OUTLIER) cc_final: 0.7461 (t60) REVERT: A 87 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.6023 (p0) REVERT: A 238 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6734 (tt0) REVERT: A 300 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8021 (tt) REVERT: B 271 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8537 (t) REVERT: B 350 TRP cc_start: 0.8661 (OUTLIER) cc_final: 0.8245 (p-90) REVERT: B 546 THR cc_start: 0.8881 (m) cc_final: 0.8668 (m) REVERT: B 954 GLN cc_start: 0.7813 (tp-100) cc_final: 0.7488 (tp-100) REVERT: C 150 MET cc_start: 0.3980 (tmm) cc_final: 0.3643 (tmm) REVERT: H 6 GLU cc_start: 0.1535 (OUTLIER) cc_final: 0.1189 (tp30) REVERT: I 92 ASP cc_start: 0.6034 (t0) cc_final: 0.5721 (t0) REVERT: J 28 ILE cc_start: 0.4255 (mp) cc_final: 0.3745 (pt) outliers start: 74 outliers final: 61 residues processed: 226 average time/residue: 0.3710 time to fit residues: 142.8006 Evaluate side-chains 225 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 157 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 620 HIS Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 218 optimal weight: 50.0000 chunk 352 optimal weight: 40.0000 chunk 215 optimal weight: 0.0980 chunk 167 optimal weight: 5.9990 chunk 244 optimal weight: 0.0670 chunk 369 optimal weight: 9.9990 chunk 340 optimal weight: 20.0000 chunk 294 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 overall best weight: 1.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 GLN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30934 Z= 0.221 Angle : 0.577 9.501 42088 Z= 0.290 Chirality : 0.045 0.337 4922 Planarity : 0.004 0.061 5360 Dihedral : 7.391 113.192 5366 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.03 % Favored : 92.84 % Rotamer: Outliers : 2.31 % Allowed : 18.17 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3714 helix: 0.03 (0.21), residues: 671 sheet: -0.56 (0.19), residues: 763 loop : -1.80 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 149 HIS 0.005 0.001 HIS B 951 PHE 0.021 0.001 PHE C 165 TYR 0.018 0.001 TYR B 393 ARG 0.009 0.000 ARG B1104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 159 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7722 (OUTLIER) cc_final: 0.7502 (t60) REVERT: A 87 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.5944 (p0) REVERT: A 238 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: B 350 TRP cc_start: 0.8644 (OUTLIER) cc_final: 0.8196 (p-90) REVERT: B 546 THR cc_start: 0.8934 (m) cc_final: 0.8724 (m) REVERT: B 954 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7460 (tp-100) REVERT: B 960 VAL cc_start: 0.9590 (OUTLIER) cc_final: 0.9321 (t) REVERT: C 124 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8211 (p) REVERT: H 6 GLU cc_start: 0.1590 (OUTLIER) cc_final: 0.1238 (tp30) REVERT: I 92 ASP cc_start: 0.6048 (t0) cc_final: 0.5633 (t0) REVERT: J 28 ILE cc_start: 0.4285 (mp) cc_final: 0.3766 (pt) outliers start: 76 outliers final: 65 residues processed: 223 average time/residue: 0.3915 time to fit residues: 150.6673 Evaluate side-chains 227 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 155 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 271 optimal weight: 8.9990 chunk 43 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 302 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 GLN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.143562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.096988 restraints weight = 76265.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098296 restraints weight = 57898.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097656 restraints weight = 42839.568| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30934 Z= 0.160 Angle : 0.553 9.446 42088 Z= 0.277 Chirality : 0.045 0.336 4922 Planarity : 0.004 0.061 5360 Dihedral : 7.156 110.853 5366 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.30 % Favored : 93.54 % Rotamer: Outliers : 2.34 % Allowed : 18.20 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3714 helix: 0.18 (0.21), residues: 682 sheet: -0.46 (0.19), residues: 750 loop : -1.76 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 149 HIS 0.005 0.001 HIS B 951 PHE 0.017 0.001 PHE C 55 TYR 0.019 0.001 TYR I 86 ARG 0.007 0.000 ARG A 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.83 seconds wall clock time: 89 minutes 10.38 seconds (5350.38 seconds total)