Starting phenix.real_space_refine on Wed Jul 24 17:46:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnq_33323/07_2024/7xnq_33323.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnq_33323/07_2024/7xnq_33323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnq_33323/07_2024/7xnq_33323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnq_33323/07_2024/7xnq_33323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnq_33323/07_2024/7xnq_33323.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnq_33323/07_2024/7xnq_33323.cif" } resolution = 3.52 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= 0.067 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 114 5.16 5 C 16854 2.51 5 N 4305 2.21 5 O 5190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A ASP 948": "OD1" <-> "OD2" Residue "A GLU 1029": "OE1" <-> "OE2" Residue "A ASP 1039": "OD1" <-> "OD2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 948": "OD1" <-> "OD2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 746": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 26463 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8499 Classifications: {'peptide': 1089} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1030} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8499 Classifications: {'peptide': 1089} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1030} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8499 Classifications: {'peptide': 1089} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1030} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "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: 14.14, per 1000 atoms: 0.53 Number of scatterers: 26463 At special positions: 0 Unit cell: (161.2, 157.04, 178.88, 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 114 16.00 O 5190 8.00 N 4305 7.00 C 16854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.02 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.02 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.04 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 164 " distance=2.04 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.02 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " 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=7, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 72 " " NAG A1303 " - " ASN A 120 " " NAG A1304 " - " ASN A 147 " " NAG A1305 " - " ASN A 163 " " NAG A1306 " - " ASN A 232 " " NAG A1307 " - " ASN A 329 " " NAG A1308 " - " ASN A 601 " " NAG A1309 " - " ASN A 614 " " NAG A1310 " - " ASN A 655 " " NAG A1311 " - " ASN A1096 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 72 " " NAG B1303 " - " ASN B 120 " " NAG B1304 " - " ASN B 147 " " NAG B1305 " - " ASN B 163 " " NAG B1306 " - " ASN B 232 " " NAG B1307 " - " ASN B 329 " " NAG B1308 " - " ASN B 601 " " NAG B1309 " - " ASN B 614 " " NAG B1310 " - " ASN B 655 " " NAG B1311 " - " ASN B1096 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 72 " " NAG C1303 " - " ASN C 120 " " NAG C1304 " - " ASN C 147 " " NAG C1305 " - " ASN C 163 " " NAG C1306 " - " ASN C 232 " " NAG C1307 " - " ASN C 329 " " NAG C1308 " - " ASN C 601 " " NAG C1309 " - " ASN C 614 " " NAG C1310 " - " ASN C 655 " " NAG C1311 " - " ASN C1096 " " NAG D 1 " - " ASN A 280 " " NAG E 1 " - " ASN A 707 " " NAG F 1 " - " ASN A 715 " " NAG G 1 " - " ASN A 799 " " NAG H 1 " - " ASN A1072 " " NAG I 1 " - " ASN A1132 " " NAG J 1 " - " ASN B 280 " " NAG K 1 " - " ASN B 707 " " NAG L 1 " - " ASN B 715 " " NAG M 1 " - " ASN B 799 " " NAG N 1 " - " ASN B1072 " " NAG O 1 " - " ASN B1132 " " NAG P 1 " - " ASN C 280 " " NAG Q 1 " - " ASN C 707 " " NAG R 1 " - " ASN C 715 " " NAG S 1 " - " ASN C 799 " " NAG T 1 " - " ASN C1072 " " NAG U 1 " - " ASN C1132 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.37 Conformation dependent library (CDL) restraints added in 4.5 seconds 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6108 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 56 sheets defined 24.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 336 through 342 removed outlier: 4.028A pdb=" N PHE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.682A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.854A pdb=" N ILE A 408 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.607A pdb=" N TYR A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.793A pdb=" N TYR A 449 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.670A pdb=" N GLN A 504 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 635 removed outlier: 3.634A pdb=" N TYR A 634 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.605A pdb=" N LEU A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.650A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 777 " --> pdb=" O ASP A 773 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 848 through 853 removed outlier: 3.757A pdb=" N LYS A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 848 through 853' Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 905 Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.770A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 removed outlier: 3.596A pdb=" N ILE A 932 " --> pdb=" O ALA A 928 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 937 " --> pdb=" O GLN A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 962 removed outlier: 3.503A pdb=" N VAL A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 966 Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.980A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'A' and resid 986 through 1030 removed outlier: 4.015A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1139 through 1148 removed outlier: 3.896A pdb=" N PHE A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A1147 " --> pdb=" O LEU A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 336 through 342 removed outlier: 4.047A pdb=" N PHE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.696A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.790A pdb=" N ILE B 408 " --> pdb=" O VAL B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.508A pdb=" N TYR B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.846A pdb=" N TYR B 449 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 450 " --> pdb=" O TYR B 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 446 through 450' Processing helix chain 'B' and resid 500 through 504 removed outlier: 3.575A pdb=" N GLN B 504 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 removed outlier: 3.634A pdb=" N TYR B 634 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 744 through 753 removed outlier: 3.691A pdb=" N LEU B 750 " --> pdb=" O GLU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 781 removed outlier: 3.541A pdb=" N ASP B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 777 " --> pdb=" O ASP B 773 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 778 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 779 " --> pdb=" O ASN B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 848 through 853 removed outlier: 3.700A pdb=" N LYS B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 853 " --> pdb=" O CYS B 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 848 through 853' Processing helix chain 'B' and resid 864 through 883 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 905 removed outlier: 3.540A pdb=" N ALA B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 917 removed outlier: 3.937A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 removed outlier: 3.603A pdb=" N ILE B 932 " --> pdb=" O ALA B 928 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 937 " --> pdb=" O GLN B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 982 removed outlier: 3.907A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 979 " --> pdb=" O LEU B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1030 removed outlier: 4.218A pdb=" N GLU B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1116 No H-bonds generated for 'chain 'B' and resid 1114 through 1116' Processing helix chain 'B' and resid 1139 through 1148 removed outlier: 3.876A pdb=" N PHE B1146 " --> pdb=" O GLU B1142 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B1147 " --> pdb=" O LEU B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 336 through 342 removed outlier: 4.055A pdb=" N PHE C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.725A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.905A pdb=" N ILE C 408 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.533A pdb=" N TYR C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.940A pdb=" N TYR C 449 " --> pdb=" O ASN C 446 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 450 " --> pdb=" O TYR C 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 446 through 450' Processing helix chain 'C' and resid 500 through 504 removed outlier: 3.615A pdb=" N GLN C 504 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 635 removed outlier: 3.610A pdb=" N TYR C 634 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 753 removed outlier: 3.675A pdb=" N LEU C 750 " --> pdb=" O GLU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.765A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 777 " --> pdb=" O ASP C 773 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 848 through 853 removed outlier: 3.710A pdb=" N LYS C 852 " --> pdb=" O ILE C 848 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE C 853 " --> pdb=" O CYS C 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 848 through 853' Processing helix chain 'C' and resid 864 through 882 removed outlier: 3.508A pdb=" N GLN C 870 " --> pdb=" O GLU C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 905 removed outlier: 3.517A pdb=" N ALA C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.867A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.579A pdb=" N ILE C 932 " --> pdb=" O ALA C 928 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN C 933 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 937 " --> pdb=" O GLN C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 removed outlier: 3.514A pdb=" N VAL C 950 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.967A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1030 removed outlier: 4.291A pdb=" N GLU C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN C 990 " --> pdb=" O GLU C 986 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 997 " --> pdb=" O ARG C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1116 No H-bonds generated for 'chain 'C' and resid 1114 through 1116' Processing helix chain 'C' and resid 1139 through 1148 removed outlier: 3.895A pdb=" N PHE C1146 " --> pdb=" O GLU C1142 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS C1147 " --> pdb=" O LEU C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.278A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 124 through 127 removed outlier: 6.131A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 274 through 276 Processing sheet with id=AA7, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.235A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 324 removed outlier: 7.714A pdb=" N GLU A 322 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ASN A 540 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 322 through 324 removed outlier: 7.714A pdb=" N GLU A 322 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ASN A 540 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 396 through 400 removed outlier: 3.624A pdb=" N ASP A 396 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 510 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 507 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 434 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB3, first strand: chain 'A' and resid 563 through 564 removed outlier: 6.542A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 574 through 575 Processing sheet with id=AB5, first strand: chain 'A' and resid 662 through 665 removed outlier: 6.784A pdb=" N ILE A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.652A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 709 through 720 removed outlier: 6.419A pdb=" N GLN A1069 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE A 716 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 718 " --> pdb=" O TYR A1065 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR A1065 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A 720 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1063 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLY A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER A1053 " --> pdb=" O GLY A1057 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A1059 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A1061 " --> pdb=" O SER A1049 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER A1049 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A1063 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 723 through 726 removed outlier: 3.578A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 731 through 733 removed outlier: 4.218A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 785 through 786 Processing sheet with id=AC2, first strand: chain 'A' and resid 1118 through 1123 removed outlier: 3.517A pdb=" N SER A1121 " --> pdb=" O ALA A1085 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA A1085 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.520A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.318A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC6, first strand: chain 'B' and resid 99 through 103 Processing sheet with id=AC7, first strand: chain 'B' and resid 116 through 119 Processing sheet with id=AC8, first strand: chain 'B' and resid 274 through 276 Processing sheet with id=AC9, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.226A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 323 through 324 removed outlier: 7.828A pdb=" N ILE B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 541 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 323 through 324 removed outlier: 7.828A pdb=" N ILE B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 396 through 400 removed outlier: 3.540A pdb=" N ASP B 396 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 510 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 400 " --> pdb=" O TYR B 506 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 506 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 507 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP B 434 " --> pdb=" O ARG B 507 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AD5, first strand: chain 'B' and resid 563 through 565 removed outlier: 6.581A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 574 through 575 Processing sheet with id=AD7, first strand: chain 'B' and resid 662 through 665 removed outlier: 6.773A pdb=" N ILE B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 699 through 702 Processing sheet with id=AD9, first strand: chain 'B' and resid 709 through 720 removed outlier: 6.717A pdb=" N GLN B1069 " --> pdb=" O THR B 714 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 716 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE B 718 " --> pdb=" O TYR B1065 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR B1065 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 720 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B1063 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B1063 " --> pdb=" O LEU B1047 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 709 through 720 removed outlier: 6.717A pdb=" N GLN B1069 " --> pdb=" O THR B 714 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 716 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE B 718 " --> pdb=" O TYR B1065 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR B1065 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 720 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B1063 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B1074 " --> pdb=" O SER B1095 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B1076 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE B1093 " --> pdb=" O ALA B1076 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 723 through 726 Processing sheet with id=AE3, first strand: chain 'B' and resid 731 through 733 removed outlier: 4.308A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 3.542A pdb=" N SER B1121 " --> pdb=" O ALA B1085 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AE6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE7, first strand: chain 'C' and resid 222 through 227 removed outlier: 6.135A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 124 through 127 removed outlier: 6.095A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 274 through 276 Processing sheet with id=AF1, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.253A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 323 through 324 removed outlier: 3.508A pdb=" N PHE C 541 " --> pdb=" O LEU C 544 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 396 through 400 removed outlier: 3.562A pdb=" N ASP C 396 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 510 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG C 507 " --> pdb=" O TRP C 434 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP C 434 " --> pdb=" O ARG C 507 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AF5, first strand: chain 'C' and resid 574 through 575 Processing sheet with id=AF6, first strand: chain 'C' and resid 662 through 665 removed outlier: 6.770A pdb=" N ILE C 668 " --> pdb=" O ILE C 664 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 709 through 720 removed outlier: 6.920A pdb=" N GLN C1069 " --> pdb=" O THR C 714 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE C 716 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE C 718 " --> pdb=" O TYR C1065 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR C1065 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 720 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1063 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL C1063 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 709 through 720 removed outlier: 6.920A pdb=" N GLN C1069 " --> pdb=" O THR C 714 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE C 716 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE C 718 " --> pdb=" O TYR C1065 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR C1065 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 720 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1063 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 723 through 726 Processing sheet with id=AG1, first strand: chain 'C' and resid 731 through 733 removed outlier: 4.223A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1118 through 1123 removed outlier: 3.552A pdb=" N SER C1121 " --> pdb=" O ALA C1085 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA C1085 " --> pdb=" O SER C1121 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 2061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.40 Time building geometry restraints manager: 11.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8357 1.34 - 1.47: 6852 1.47 - 1.59: 11734 1.59 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 27087 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N THR C 331 " pdb=" CA THR C 331 " ideal model delta sigma weight residual 1.459 1.488 -0.028 9.10e-03 1.21e+04 9.70e+00 bond pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.25e-02 6.40e+03 9.02e+00 bond pdb=" N VAL C 360 " pdb=" CA VAL C 360 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.22e-02 6.72e+03 8.46e+00 bond pdb=" N ILE B 330 " pdb=" CA ILE B 330 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.25e-02 6.40e+03 8.38e+00 ... (remaining 27082 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.78: 614 105.78 - 112.83: 14680 112.83 - 119.89: 8527 119.89 - 126.94: 12818 126.94 - 134.00: 252 Bond angle restraints: 36891 Sorted by residual: angle pdb=" N SER B 528 " pdb=" CA SER B 528 " pdb=" C SER B 528 " ideal model delta sigma weight residual 110.50 104.99 5.51 1.41e+00 5.03e-01 1.53e+01 angle pdb=" N SER C 528 " pdb=" CA SER C 528 " pdb=" C SER C 528 " ideal model delta sigma weight residual 110.53 105.50 5.03 1.32e+00 5.74e-01 1.45e+01 angle pdb=" CA LEU C 333 " pdb=" C LEU C 333 " pdb=" O LEU C 333 " ideal model delta sigma weight residual 121.44 117.51 3.93 1.08e+00 8.57e-01 1.33e+01 angle pdb=" C CYS C 359 " pdb=" CA CYS C 359 " pdb=" CB CYS C 359 " ideal model delta sigma weight residual 114.87 109.38 5.49 1.51e+00 4.39e-01 1.32e+01 angle pdb=" CA LEU B 333 " pdb=" C LEU B 333 " pdb=" O LEU B 333 " ideal model delta sigma weight residual 121.44 117.54 3.90 1.08e+00 8.57e-01 1.30e+01 ... (remaining 36886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 15814 22.40 - 44.79: 973 44.79 - 67.19: 144 67.19 - 89.59: 45 89.59 - 111.98: 16 Dihedral angle restraints: 16992 sinusoidal: 7479 harmonic: 9513 Sorted by residual: dihedral pdb=" CB CYS B 660 " pdb=" SG CYS B 660 " pdb=" SG CYS B 669 " pdb=" CB CYS B 669 " ideal model delta sinusoidal sigma weight residual 93.00 10.01 82.99 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual 93.00 10.22 82.78 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS A 660 " pdb=" SG CYS A 660 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual -86.00 -5.22 -80.78 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 16989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4147 0.101 - 0.201: 198 0.201 - 0.302: 5 0.302 - 0.402: 2 0.402 - 0.503: 4 Chirality restraints: 4356 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 147 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 147 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 147 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 4353 not shown) Planarity restraints: 4743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 525 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C PRO B 525 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO B 525 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS B 526 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 525 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C PRO C 525 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO C 525 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS C 526 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 525 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C PRO A 525 " -0.049 2.00e-02 2.50e+03 pdb=" O PRO A 525 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 526 " 0.017 2.00e-02 2.50e+03 ... (remaining 4740 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 573 2.68 - 3.23: 25833 3.23 - 3.79: 39764 3.79 - 4.34: 53393 4.34 - 4.90: 86984 Nonbonded interactions: 206547 Sorted by model distance: nonbonded pdb=" OG SER A 756 " pdb=" OE1 GLN C 963 " model vdw 2.121 2.440 nonbonded pdb=" OG1 THR A1114 " pdb=" OD1 ASP A1116 " model vdw 2.190 2.440 nonbonded pdb=" OG1 THR B1114 " pdb=" OD1 ASP B1116 " model vdw 2.201 2.440 nonbonded pdb=" OG1 THR C1114 " pdb=" OD1 ASP C1116 " model vdw 2.208 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.209 2.440 ... (remaining 206542 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 71.150 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.140 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 : 0.004 0.083 27087 Z= 0.236 Angle : 0.627 7.820 36891 Z= 0.331 Chirality : 0.049 0.503 4356 Planarity : 0.005 0.069 4692 Dihedral : 14.677 111.983 10776 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 0.49 % Allowed : 0.35 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3249 helix: -0.07 (0.20), residues: 630 sheet: -1.00 (0.22), residues: 495 loop : -1.92 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 631 HIS 0.013 0.001 HIS B 517 PHE 0.028 0.001 PHE B 65 TYR 0.026 0.001 TYR A 158 ARG 0.003 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 354 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7562 (m-10) cc_final: 0.7348 (m-80) REVERT: A 151 MET cc_start: 0.5297 (ttt) cc_final: 0.5072 (mmm) REVERT: A 337 ASP cc_start: 0.7916 (p0) cc_final: 0.7566 (p0) REVERT: A 385 LEU cc_start: 0.8482 (mt) cc_final: 0.8104 (mt) REVERT: A 594 SER cc_start: 0.9058 (p) cc_final: 0.8853 (p) REVERT: A 719 SER cc_start: 0.8771 (t) cc_final: 0.8210 (p) REVERT: A 753 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 963 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 1120 VAL cc_start: 0.8972 (t) cc_final: 0.8591 (p) REVERT: B 308 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8717 (tttm) REVERT: B 337 ASP cc_start: 0.7939 (p0) cc_final: 0.7535 (p0) REVERT: B 385 LEU cc_start: 0.8474 (mt) cc_final: 0.8168 (mt) REVERT: B 491 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 719 SER cc_start: 0.8664 (t) cc_final: 0.7962 (p) REVERT: B 852 LYS cc_start: 0.7104 (mmtm) cc_final: 0.6884 (tttm) REVERT: B 1000 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7003 (tm-30) REVERT: B 1027 MET cc_start: 0.8665 (tpp) cc_final: 0.8457 (tpp) REVERT: C 218 PHE cc_start: 0.6757 (t80) cc_final: 0.6311 (t80) REVERT: C 337 ASP cc_start: 0.7957 (p0) cc_final: 0.7733 (p0) REVERT: C 385 LEU cc_start: 0.8593 (mt) cc_final: 0.8158 (mt) REVERT: C 491 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7534 (tm-30) REVERT: C 852 LYS cc_start: 0.7046 (mmtm) cc_final: 0.6809 (tttp) REVERT: C 1048 MET cc_start: 0.7902 (ptm) cc_final: 0.7637 (ptt) outliers start: 14 outliers final: 3 residues processed: 368 average time/residue: 0.3835 time to fit residues: 227.3213 Evaluate side-chains 183 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 180 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 392 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 253 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 154 optimal weight: 20.0000 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN A 955 GLN B 953 ASN B 955 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 760 GLN C 893 GLN C 911 GLN C 953 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27087 Z= 0.326 Angle : 0.643 8.355 36891 Z= 0.327 Chirality : 0.047 0.458 4356 Planarity : 0.005 0.099 4692 Dihedral : 8.851 97.865 4964 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.37 % Allowed : 8.99 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3249 helix: 0.45 (0.20), residues: 639 sheet: -1.33 (0.20), residues: 561 loop : -1.99 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 884 HIS 0.007 0.001 HIS B 517 PHE 0.022 0.002 PHE A 557 TYR 0.021 0.002 TYR B1065 ARG 0.005 0.000 ARG C 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 211 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7811 (m-10) cc_final: 0.7414 (m-80) REVERT: A 151 MET cc_start: 0.5365 (ttt) cc_final: 0.5138 (mmm) REVERT: A 301 LEU cc_start: 0.8875 (tp) cc_final: 0.8643 (tt) REVERT: A 385 LEU cc_start: 0.8520 (mt) cc_final: 0.8099 (mt) REVERT: A 719 SER cc_start: 0.8611 (t) cc_final: 0.8012 (p) REVERT: A 753 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 963 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A 1120 VAL cc_start: 0.9024 (t) cc_final: 0.8701 (p) REVERT: B 131 PHE cc_start: 0.6478 (m-80) cc_final: 0.6213 (m-80) REVERT: B 363 TYR cc_start: 0.7733 (m-80) cc_final: 0.7480 (m-80) REVERT: B 385 LEU cc_start: 0.8485 (mt) cc_final: 0.8010 (mt) REVERT: B 491 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7455 (tm-30) REVERT: B 1011 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8465 (mp) REVERT: C 385 LEU cc_start: 0.8548 (mt) cc_final: 0.8193 (mt) REVERT: C 491 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7445 (tm-30) REVERT: C 659 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 852 LYS cc_start: 0.7149 (mmtm) cc_final: 0.6944 (tttp) REVERT: C 971 ILE cc_start: 0.9049 (mp) cc_final: 0.8822 (mm) REVERT: C 1027 MET cc_start: 0.8773 (tpp) cc_final: 0.8552 (tpt) REVERT: C 1120 VAL cc_start: 0.8978 (t) cc_final: 0.8690 (p) outliers start: 39 outliers final: 24 residues processed: 239 average time/residue: 0.3447 time to fit residues: 136.3542 Evaluate side-chains 183 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1025 THR Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1025 THR Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.4980 chunk 91 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 294 optimal weight: 0.9990 chunk 318 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 292 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 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 415 ASN ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27087 Z= 0.181 Angle : 0.548 9.002 36891 Z= 0.278 Chirality : 0.045 0.436 4356 Planarity : 0.005 0.107 4692 Dihedral : 7.240 93.438 4958 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.52 % Allowed : 11.24 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 3249 helix: 0.86 (0.20), residues: 633 sheet: -1.26 (0.20), residues: 567 loop : -1.86 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 884 HIS 0.005 0.001 HIS B 517 PHE 0.024 0.001 PHE B 199 TYR 0.018 0.001 TYR B1136 ARG 0.005 0.000 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 182 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7653 (m-10) cc_final: 0.7431 (m-10) REVERT: A 151 MET cc_start: 0.5380 (ttt) cc_final: 0.5114 (mmm) REVERT: A 719 SER cc_start: 0.8583 (t) cc_final: 0.7979 (p) REVERT: A 753 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8004 (tm-30) REVERT: A 866 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 963 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7213 (tm-30) REVERT: A 1120 VAL cc_start: 0.8946 (t) cc_final: 0.8634 (p) REVERT: B 308 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8919 (tttt) REVERT: B 385 LEU cc_start: 0.8519 (mt) cc_final: 0.8247 (mt) REVERT: B 866 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 1011 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8478 (mp) REVERT: C 385 LEU cc_start: 0.8566 (mt) cc_final: 0.8195 (mt) REVERT: C 971 ILE cc_start: 0.9010 (mp) cc_final: 0.8785 (mm) REVERT: C 1120 VAL cc_start: 0.8918 (t) cc_final: 0.8625 (p) outliers start: 43 outliers final: 30 residues processed: 214 average time/residue: 0.3487 time to fit residues: 124.6958 Evaluate side-chains 184 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1121 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 1025 THR Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 313 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 280 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN B 194 ASN B 760 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27087 Z= 0.341 Angle : 0.600 9.285 36891 Z= 0.304 Chirality : 0.046 0.419 4356 Planarity : 0.005 0.076 4692 Dihedral : 6.890 91.729 4958 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.50 % Allowed : 12.76 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3249 helix: 0.80 (0.20), residues: 642 sheet: -1.47 (0.19), residues: 585 loop : -1.87 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 631 HIS 0.005 0.001 HIS C1046 PHE 0.021 0.002 PHE C 557 TYR 0.017 0.002 TYR B1065 ARG 0.005 0.001 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 166 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8045 (m) REVERT: A 719 SER cc_start: 0.8667 (t) cc_final: 0.8055 (p) REVERT: A 753 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 866 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 1120 VAL cc_start: 0.8991 (t) cc_final: 0.8731 (p) REVERT: B 272 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7763 (m) REVERT: B 363 TYR cc_start: 0.7746 (m-80) cc_final: 0.7476 (m-80) REVERT: B 385 LEU cc_start: 0.8530 (mt) cc_final: 0.8162 (mt) REVERT: B 491 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7404 (tm-30) REVERT: B 866 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 1011 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8513 (mp) REVERT: C 272 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7840 (m) REVERT: C 385 LEU cc_start: 0.8609 (mt) cc_final: 0.8233 (mt) REVERT: C 971 ILE cc_start: 0.9072 (mp) cc_final: 0.8871 (mm) REVERT: C 1120 VAL cc_start: 0.8965 (t) cc_final: 0.8716 (p) outliers start: 71 outliers final: 52 residues processed: 221 average time/residue: 0.3230 time to fit residues: 121.7750 Evaluate side-chains 209 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 153 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1121 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 991 ILE Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1121 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 991 ILE Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1025 THR Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1112 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.2980 chunk 177 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 129 optimal weight: 0.0670 chunk 267 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 0.0970 chunk 281 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN C 753 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27087 Z= 0.145 Angle : 0.526 9.684 36891 Z= 0.264 Chirality : 0.044 0.411 4356 Planarity : 0.004 0.069 4692 Dihedral : 6.254 89.135 4958 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.90 % Allowed : 13.46 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3249 helix: 1.27 (0.20), residues: 636 sheet: -1.51 (0.19), residues: 606 loop : -1.79 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 631 HIS 0.004 0.001 HIS A 517 PHE 0.035 0.001 PHE C 199 TYR 0.016 0.001 TYR C1136 ARG 0.004 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 190 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.4370 (mmm) cc_final: 0.3612 (mpp) REVERT: A 719 SER cc_start: 0.8657 (t) cc_final: 0.8048 (p) REVERT: A 753 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 866 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 963 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7139 (tm-30) REVERT: A 1120 VAL cc_start: 0.8928 (t) cc_final: 0.8637 (p) REVERT: B 201 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6685 (tt) REVERT: B 272 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7660 (m) REVERT: B 308 LYS cc_start: 0.9267 (ttmt) cc_final: 0.8920 (tttt) REVERT: B 385 LEU cc_start: 0.8504 (mt) cc_final: 0.8170 (mt) REVERT: B 491 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 866 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 1011 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8497 (mp) REVERT: C 272 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7772 (m) REVERT: C 385 LEU cc_start: 0.8568 (mt) cc_final: 0.8193 (mt) REVERT: C 1120 VAL cc_start: 0.8888 (t) cc_final: 0.8600 (p) outliers start: 54 outliers final: 31 residues processed: 225 average time/residue: 0.3344 time to fit residues: 126.8658 Evaluate side-chains 198 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1121 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 8.9990 chunk 282 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 313 optimal weight: 0.0170 chunk 260 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 103 optimal weight: 0.0970 chunk 164 optimal weight: 5.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN C 530 ASN C 753 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27087 Z= 0.156 Angle : 0.519 9.892 36891 Z= 0.259 Chirality : 0.044 0.402 4356 Planarity : 0.004 0.064 4692 Dihedral : 5.917 87.185 4956 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.90 % Allowed : 14.24 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3249 helix: 1.45 (0.21), residues: 636 sheet: -1.46 (0.20), residues: 606 loop : -1.76 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 631 HIS 0.004 0.001 HIS A 517 PHE 0.021 0.001 PHE A 90 TYR 0.019 0.001 TYR C1136 ARG 0.004 0.000 ARG A1105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 170 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.4386 (mmm) cc_final: 0.3675 (mpp) REVERT: A 272 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8075 (m) REVERT: A 385 LEU cc_start: 0.8619 (mt) cc_final: 0.8366 (tt) REVERT: A 491 GLN cc_start: 0.7366 (tm-30) cc_final: 0.7109 (tm-30) REVERT: A 719 SER cc_start: 0.8595 (t) cc_final: 0.7983 (p) REVERT: A 753 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 866 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 963 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7095 (tm-30) REVERT: A 1120 VAL cc_start: 0.8939 (t) cc_final: 0.8662 (p) REVERT: B 199 PHE cc_start: 0.6395 (t80) cc_final: 0.6194 (t80) REVERT: B 201 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6612 (tt) REVERT: B 272 THR cc_start: 0.7946 (OUTLIER) cc_final: 0.7716 (m) REVERT: B 308 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8858 (tttt) REVERT: B 385 LEU cc_start: 0.8438 (mt) cc_final: 0.8071 (mt) REVERT: B 491 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 866 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7716 (tm-30) REVERT: B 1011 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8498 (mp) REVERT: C 272 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7785 (m) REVERT: C 385 LEU cc_start: 0.8560 (mt) cc_final: 0.8195 (mt) REVERT: C 1120 VAL cc_start: 0.8907 (t) cc_final: 0.8637 (p) outliers start: 54 outliers final: 40 residues processed: 208 average time/residue: 0.3296 time to fit residues: 116.5076 Evaluate side-chains 205 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 160 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1121 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain B residue 1121 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 178 optimal weight: 5.9990 chunk 228 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 312 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27087 Z= 0.153 Angle : 0.515 10.254 36891 Z= 0.257 Chirality : 0.043 0.392 4356 Planarity : 0.004 0.063 4692 Dihedral : 5.607 84.074 4956 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.36 % Allowed : 14.34 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 3249 helix: 1.58 (0.21), residues: 636 sheet: -1.42 (0.20), residues: 606 loop : -1.71 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 631 HIS 0.004 0.000 HIS B 517 PHE 0.032 0.001 PHE C 199 TYR 0.017 0.001 TYR C1136 ARG 0.003 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 173 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.8051 (m) REVERT: A 363 TYR cc_start: 0.7503 (m-80) cc_final: 0.7094 (m-80) REVERT: A 385 LEU cc_start: 0.8595 (mt) cc_final: 0.8382 (tt) REVERT: A 491 GLN cc_start: 0.7323 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 719 SER cc_start: 0.8587 (t) cc_final: 0.7991 (p) REVERT: A 753 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8024 (tm-30) REVERT: A 866 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 1120 VAL cc_start: 0.8900 (t) cc_final: 0.8643 (p) REVERT: B 201 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6747 (tt) REVERT: B 272 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7794 (m) REVERT: B 308 LYS cc_start: 0.9210 (ttmt) cc_final: 0.8833 (tttt) REVERT: B 385 LEU cc_start: 0.8405 (mt) cc_final: 0.8054 (mt) REVERT: B 491 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 866 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 1011 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8516 (mp) REVERT: C 272 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7734 (m) REVERT: C 385 LEU cc_start: 0.8559 (mt) cc_final: 0.8194 (mt) REVERT: C 902 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.5696 (m-80) REVERT: C 1120 VAL cc_start: 0.8930 (t) cc_final: 0.8648 (p) outliers start: 67 outliers final: 48 residues processed: 224 average time/residue: 0.3169 time to fit residues: 122.3539 Evaluate side-chains 213 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 159 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1121 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1121 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 902 TYR Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 chunk 154 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 245 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 27087 Z= 0.425 Angle : 0.645 10.488 36891 Z= 0.325 Chirality : 0.047 0.374 4356 Planarity : 0.005 0.062 4692 Dihedral : 6.020 81.666 4956 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.64 % Allowed : 14.38 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.14), residues: 3249 helix: 1.00 (0.20), residues: 642 sheet: -1.64 (0.19), residues: 660 loop : -1.79 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 631 HIS 0.007 0.001 HIS B1046 PHE 0.026 0.002 PHE C 557 TYR 0.023 0.002 TYR C 754 ARG 0.008 0.001 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 163 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8137 (m) REVERT: A 363 TYR cc_start: 0.7577 (m-80) cc_final: 0.7325 (m-80) REVERT: A 385 LEU cc_start: 0.8589 (mt) cc_final: 0.8301 (tt) REVERT: A 491 GLN cc_start: 0.7280 (tm-30) cc_final: 0.7034 (tm-30) REVERT: A 719 SER cc_start: 0.8624 (t) cc_final: 0.8016 (p) REVERT: A 753 GLN cc_start: 0.8526 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 866 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 1120 VAL cc_start: 0.9007 (t) cc_final: 0.8783 (p) REVERT: B 272 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7927 (m) REVERT: B 385 LEU cc_start: 0.8490 (mt) cc_final: 0.8128 (mt) REVERT: B 491 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7480 (tm-30) REVERT: B 566 ASP cc_start: 0.6840 (p0) cc_final: 0.3773 (m-30) REVERT: B 866 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 385 LEU cc_start: 0.8641 (mt) cc_final: 0.8267 (mt) REVERT: C 513 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7349 (p90) REVERT: C 902 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.5807 (m-80) outliers start: 75 outliers final: 54 residues processed: 223 average time/residue: 0.3463 time to fit residues: 130.7640 Evaluate side-chains 215 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 157 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1121 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1121 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 902 TYR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 991 ILE Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.6980 chunk 299 optimal weight: 0.9980 chunk 272 optimal weight: 0.8980 chunk 291 optimal weight: 0.3980 chunk 175 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 228 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 289 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27087 Z= 0.172 Angle : 0.545 10.642 36891 Z= 0.272 Chirality : 0.044 0.381 4356 Planarity : 0.004 0.061 4692 Dihedral : 5.663 79.490 4956 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.22 % Allowed : 15.15 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3249 helix: 1.42 (0.21), residues: 639 sheet: -1.50 (0.20), residues: 633 loop : -1.72 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 631 HIS 0.004 0.001 HIS B 517 PHE 0.031 0.001 PHE C 199 TYR 0.024 0.001 TYR A 158 ARG 0.004 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 148 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8040 (m) REVERT: A 363 TYR cc_start: 0.7586 (m-80) cc_final: 0.7379 (m-80) REVERT: A 385 LEU cc_start: 0.8622 (mt) cc_final: 0.8313 (tt) REVERT: A 491 GLN cc_start: 0.7253 (tm-30) cc_final: 0.7041 (tm-30) REVERT: A 719 SER cc_start: 0.8650 (t) cc_final: 0.8055 (p) REVERT: A 753 GLN cc_start: 0.8582 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 866 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7632 (tm-30) REVERT: A 1120 VAL cc_start: 0.8937 (t) cc_final: 0.8677 (p) REVERT: B 272 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7846 (m) REVERT: B 385 LEU cc_start: 0.8481 (mt) cc_final: 0.8186 (mt) REVERT: B 491 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7513 (tm-30) REVERT: B 866 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 1011 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8481 (mp) REVERT: C 385 LEU cc_start: 0.8625 (mt) cc_final: 0.8295 (mt) REVERT: C 719 SER cc_start: 0.8722 (t) cc_final: 0.8097 (p) REVERT: C 902 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.5861 (m-80) outliers start: 63 outliers final: 48 residues processed: 198 average time/residue: 0.3302 time to fit residues: 111.9344 Evaluate side-chains 197 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 145 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1121 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain B residue 1121 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 902 TYR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.8980 chunk 307 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 322 optimal weight: 0.9980 chunk 297 optimal weight: 3.9990 chunk 257 optimal weight: 0.3980 chunk 26 optimal weight: 0.0050 chunk 198 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27087 Z= 0.158 Angle : 0.529 10.901 36891 Z= 0.264 Chirality : 0.043 0.375 4356 Planarity : 0.004 0.058 4692 Dihedral : 5.383 76.121 4956 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.01 % Allowed : 15.36 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 3249 helix: 1.65 (0.21), residues: 636 sheet: -1.44 (0.20), residues: 633 loop : -1.70 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 631 HIS 0.004 0.001 HIS A 517 PHE 0.026 0.001 PHE A 90 TYR 0.024 0.001 TYR C 754 ARG 0.004 0.000 ARG A 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 158 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8038 (m) REVERT: A 363 TYR cc_start: 0.7575 (m-80) cc_final: 0.7287 (m-80) REVERT: A 385 LEU cc_start: 0.8585 (mt) cc_final: 0.8269 (tt) REVERT: A 719 SER cc_start: 0.8651 (t) cc_final: 0.8054 (p) REVERT: A 753 GLN cc_start: 0.8549 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 866 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 1120 VAL cc_start: 0.8889 (t) cc_final: 0.8649 (p) REVERT: B 272 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7816 (m) REVERT: B 385 LEU cc_start: 0.8451 (mt) cc_final: 0.8060 (mt) REVERT: B 491 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 866 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 1011 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8450 (mp) REVERT: C 65 PHE cc_start: 0.7598 (m-10) cc_final: 0.7320 (m-10) REVERT: C 385 LEU cc_start: 0.8600 (mt) cc_final: 0.8250 (mt) REVERT: C 719 SER cc_start: 0.8735 (t) cc_final: 0.8106 (p) REVERT: C 902 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.5762 (m-80) outliers start: 57 outliers final: 46 residues processed: 205 average time/residue: 0.3330 time to fit residues: 117.9156 Evaluate side-chains 200 residues out of total 2853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 150 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1121 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1121 SER Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 902 TYR Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 264 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN C1003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.164056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115571 restraints weight = 47608.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112191 restraints weight = 49578.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107895 restraints weight = 35805.506| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27087 Z= 0.353 Angle : 0.611 11.144 36891 Z= 0.306 Chirality : 0.046 0.363 4356 Planarity : 0.005 0.061 4692 Dihedral : 5.603 70.856 4956 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.18 % Allowed : 15.72 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3249 helix: 1.25 (0.20), residues: 636 sheet: -1.63 (0.19), residues: 660 loop : -1.77 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 256 HIS 0.006 0.001 HIS B1046 PHE 0.032 0.002 PHE C 199 TYR 0.019 0.002 TYR C1065 ARG 0.007 0.001 ARG B 813 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4414.83 seconds wall clock time: 81 minutes 10.37 seconds (4870.37 seconds total)